Marine stations have continued to contribute significantly to understanding the physiology, taxonomy, development, ecology, and evolution of animals. There are more than 50 marine stations of national universities in Japan, and historically their establishments were closely related to the initial stage of zoology in the country. More than 10 years ago, Japanese Association for Marine Biology (JAMBIO) was established to facilitate the collaboration among marine stations in the activities of research, education and administration. One of the successful activities of JAMBIO that contribute to zoology is the JAMBIO Coastal Organism Joint Surveys, in which scientists and students at multiple marine stations, as well as those from research institutes or museums, stay at a marine station for a few days, and collect and make a record of marine organisms. As of 2021, 22 surveys have been performed and new species have been reported from taxa such as Cnidaria, Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, and Echinodermata.

Taxonomic studies on marine invertebrates have been prominent in Japan since the 19th century. Globally, taxonomy was reported to have been in recession since the early 21st century, but it is not clear if it is still in hardship or is making a recovery in recent years in Japan. In order to comprehend the status quo of taxonomic studies on marine invertebrates in Japan, we compiled a list of marine invertebrate species newly described from the exclusive economic zone of this country during the period between 2003 and 2020 and investigated trends by making comparisons of higher taxa and academic journals in terms of the numbers of new species and taxonomic authors. We noticed that recruitment of new researchers into taxonomic studies is evident in some taxa. We also found that certain articles with descriptions of new species are now being published in journals aimed at general biology/zoology, not oriented principally to taxonomy. We consider from our analyses that taxonomic studies on marine invertebrates in Japan show signs of resurgence, but development of new taxonomists is awaited in certain taxa.

A literature-based list of sea spiders (pycnogonids) recorded in Japanese waters since 1891 is provided. The list includes a comprehensive collection of sampling records with geographical and bathymetric data. The present list reveals that 171 species of pycnogonids in 34 genera and 11 families have been recorded in Japanese waters. From the last comprehensive counting in 1991, 17 species have been added to the list of Japanese pycnogonid fauna over the past 30 years. The present species number nearly reaches the previously estimated species number (173 spp. in 2010). However, more species are expected in further collections from abyssal and even shallow waters.

Japan has many coastal carbon dioxide seeps as it is one of the most volcanically active parts of the world. These shallow seeps do not have the spectacular aggregations of specialist fauna seen in deep-sea vent systems but they do have gradients in seawater carbonate chemistry that are useful as natural analogues of the effects of ocean acidification on marine biodiversity, ecosystem function and fisheries. Here, we compare macroinvertebrate diversity and abundance on rocky habitats at ambient (mean ≤ 410 µatm) and high (mean 971–1484 µatm) levels of seawater pCO₂ in the warm-temperate region of Japan, avoiding areas with toxic sulphur or warm-water conditions. We show that although 70% of intertidal taxa and 40% of shallow subtidal taxa were able to tolerate the high CO₂ conditions, there was a marked reduction in the abundance of corals, bivalves and gastropods in acidified conditions. A narrower range of filter feeders, grazers, detritivores, scavengers and carnivores were present at high CO₂ resulting in a simplified coastal system that was unable to retain the high standing stocks of marine carbon biomass found in ambient conditions. It is clear that cuts in CO₂ emissions would reduce the risks of climate change and ocean acidification impacts on marine biodiversity, shellfish production and biomass in the rocky coastal shores of this region.

Sagami Bay and Suruga Bay harbor a rich marine biodiversity; however, their outer-shelf scleractinian coral fauna has not been characterized to date. Scleractinian corals were collected by dredge sampling of the Japanese Association for Marine Biology (JAMBIO) Coastal Organisms Joint Surveys in 2015 to elucidate the diversity of azooxanthellate scleractinian corals from the outer shelf zones of Sagami Bay and Suruga Bay. In this study, a total of 1291 azooxanthellate scleractinian specimens were collected, corresponding to 23 genera and 18 species, five of which are new records for Sagami Bay and eight are new records for Suruga Bay. Moreover, in all localities, except sampling locality (SL) 8, more than 70% of the specimens showed asexual reproduction. This finding suggests that asexual reproduction may play an important role in increasing the coral population size in soft-substrate environments of the outer shelf.

We performed molecular phylogenetic analyses using nucleotide sequence data from five genes (16S rRNA, cytochrome c oxidase subunit I, 18S rRNA, 28S rRNA, histone H3) determined from 36 specimens representing 25 (10 named, 15 unnamed) species of lineid heteronemerteans collected in Sagami Bay, Japan, along with other sequences obtained from public databases. External features of the 25 species are briefly described and illustrated. Lineus fuscoviridis Takakura, 1898 is transferred to Notospermus Huschke, 1830. Our molecular analysis indicated that one of our Notospermus specimens from Sagami Bay and material previously collected from the Seto Inland Sea are conspecific with Notospermus geniculatus (Delle Chiaje, 1822) s. str. [the year of publication is not 1828 as previously regarded], originally described from Naples, Italy. The new species Siphonenteron nakanoi is established; our tree shows it as the sister taxon to Siphonenteron bilineatum Renier in Meneghini, 1847; it differs from the latter in having more diffuse, scattered yellow pigmentation at the anterolateral margin of the head on each side. Pros and cons of lumping and splitting Lineidae in future studies are discussed.

The palaeonemertean genus Tubulanus Renier, 1804 currently harbors 35 species inhabiting the intertidal to the hadal zones. During a faunal survey in Sagami Bay, Japan, a single specimen of undescribed tubulanid having uniformly pale-colored body with a single dark-colored stripe on the dorsal surface was collected by dredging at depths of 116–211 m. Based on the body coloration and some anatomical features, it can be differentiated from the 35 congeners and is thus described herein as Tubulanus misakiensis sp. nov. In a molecular phylogenetic tree constructed with sequences available in public databases representing five markers (16S rRNA, cytochrome c oxidase subunit I [COI], 18S rRNA, 28S rRNA [not obtained for T. misakiensis], and histone H3), T. misakiensis was sister to Tubulanus izuensis Hookabe, Asai, Nakano, Kimura and Kajihara, 2020 and nested within a clade along with seven unidentified specimens from the abyssal and hadal zones (3428–9577 m); T. misakiensis and T. izuensis differed by 11.7% uncorrected p-distance in terms of 657-bp COI sequences.

Ctenostome bryozoans were collected from depths of 150–300 m in Suruga Bay, the Kumano Sea, and off Sendai Bay on the Pacific coast of Japan. Among these samples were five new species, three of which were epibiotic on other animals. Alcyonidium clavum n. sp., found encrusting cirri of the stalked crinoid Metacrinus rotundus, was previously reported in Japan as Alcyonidium mamillatum, but differs from the latter in lacking rings on the peristome. Triticella parvacrista n. sp. and Triticella cunabula n. sp. were epibiotic on the isopod Bathynomus doederleini and the pycnogonid Ascorhynchus japonicum, respectively. This is the first record of the genus Triticella from Japanese waters. These species differ from previously described species in autozooidal morphology, particularly the dimensions of the autozooidal dilatation, in the presence or absence of the frenaculum, and in the septate junction between the dilatation and pedicel. Bockiella arcatumida n. sp., found as erect colonies on pebbles and hydroids collected off Sendai Bay, differs from previously known species in the size and arrangement of the kenozoids in the branch. Metalcyonidium morum n. sp., collected southwest of the Izu Peninsula, occurred as small colonies having a peduncle of short kenozooids. This is the first record from the northwestern Pacific for both the genus Metalcyonidium and the family Clavoporidae. Metalcyonidium morum n. sp differs from Metalcyonidium gautieri, the only other species known in the genus, in having the capitulum divided into two parts, and in the length of the kenozooids comprising the peduncle.

A new species of amphinomid polychaete, Branchamphinome kohtsukai sp. nov., is described from Japanese waters, 29–211 m in depth. The species is distinguishable from other congeners by the following features: i) branchiae with four–six filaments in midbody segments; ii) two pairs of eyes not coalescent; iii) the ventral side of the first four chaetigers broadly pigmented. This is the first record of Branchamphinome from the North Pacific Ocean. We provide a phylogenetic tree based on the sequences of four genes (COI, 16S, 18S, 28S) and discuss amphinomids' relationships.

We describe three free-living marine nematode species from Sagami Bay, Japan. Wiesoncholaimus jambiosp. nov. is the second species of this genus. It differs from the type species, Wiesoncholaimus mawsonae Inglis, 1966, by its dorsal tooth, which is as long as the other two teeth; its conico-cylindrical tail, which is as long as 4.6–4.8 cloacal body diameters; and the absence of the gubernaculum. Thalassironus cf. britannicus de Man, 1889 agrees well with a redescription of Thalassironus britannicus de Man, 1889 based on specimens collected near the type locality. However, as it is possible that T. britannicus sensu lato includes two or more species, our species may not be conspecific to T. britannicus sensu stricto. Vasostoma cf. longispicula Huang and Wu, 2010 closely resembles Vasostoma longispicula Huang and Wu, 2010 originally described from China, but minor differentiations are observed in body diameter, body cuticle thickness, and type of precloacal supplements.

A new species of the family Splanchnotrophidae Norman and Scott, 1906 (Cyclopoida) is described based on both sexes collected from off the Oki Islands, the Sea of Japan. Specimens of both sexes of Ceratosomicola oki n. sp. were found in the body cavities of Glossodoris misakinosibogae Baba, 1988 (Nudibranchia: Chromodorididae). The copepod is characterized by the following female characters: the cephalosome with a pair of dorsolateral horn-like processes; the prosome with hemispherical posterolateral lobes on the middle region. Non-destructive, micro-computed tomography (micro-CT) imaging performed on a single specimen of the nudibranch revealed a heavy infection by a total 17 specimens of C. oki n. sp. Almost all individuals of the copepod were attached on the surface of the middle to posterior parts of the visceral sac, forming a dense cluster. The four females bearing developed lateral processes on the prosome faced the anterior end of the visceral sac and positioned the posterior tip of the body under the secondary gills of the host. The males fitted in the gaps between the females' bodies. Further, the distribution and shape of the reproductive organs of both sexes were partially clarified by micro-CT imaging.

Gnathiid larvae (Crustacea; Isopoda; Gnathiidae) infesting elasmobranch and holocephalan fishes from mainly bathyal depths off Suruga Bay, off Kume-jima Island, and five sites from off Tokyo Bay to Shimoda City, Japan were examined. A total of 1460 gnathiid larvae were sampled from 87 host individuals belonging to seven families and 10 species. The morphology of these larvae was distinguishable from other gnathiid species by the head appendages. These larvae presented two pigmentation patterns, stripes or spots, on their dorsal thoraxes in live specimens. Furthermore, they were determined as the second and third stage praniza larvae on the basis of allometric variance of maximum head and abdomen widths. A third stage praniza with stripe pigmentation metamorphosed into an adult male and could be identified as a new species of the genus Thaumastognathia Monod, 1926. The duration between detachment from the host and metamorphosis into male adult required 204 days. This paper describes Thaumastognathia bicorniger sp. nov. on the basis of P3/stripe larvae and the male adult. This report is the first record of the larva and host information for a species of Thaumastognathia.

We describe a new typhlotanaid species, Hamatipeda kohtsukai sp. nov., collected from between 167 and 488 m depth in the Sagami Sea, Japan. This is the first record of Hamatipeda from the northern hemisphere. Hamatipeda kohtsukai resembles Hamatipeda trapezoida from the Subantarctic region in having pereonites 1–3 widest anteriorly (not rectangular), but differs from it in the length ratio of antennal articles 4/5; the number of setae on the dactyli of pereopods 1–3, ischia of pereopods 4–6, and carpi of pereopods 4–6; the shape of the unguis of pereopods 4–6; and the shape of the uropodal endopod. We determined partial sequences for the cytochrome c oxidase subunit I (COI; cox1) and 18S rRNA (18S) genes in H. kohtsukai. A phylogenetic reconstruction based on the 18S sequences recovered a highly supported Typhlotanaidae clade containing H. kohtsukai and Typhlotanais mixtus, with Paranarthrura sp. (Agathotanaidae) as the sister taxon. A key to species of Hamatipeda is presented.

Acoels, belonging to Xenacoelomorpha, are small worms with a relatively simple body plan and are considered a critical clade for understanding the evolution of bilaterians. Despite acoels' importance, however, many undiscovered species are predicted to be present worldwide. Here, we describe a new marine acoel species, Amphiscolops oni sp. nov., based on materials collected from the intertidal and subtidal zones of rocky shores at several localities along the Japanese Pacific coast. The new species is approximately 3 mm long and shows typical characteristics of the family Convolutidae, such as the presence of eyespots, symbiosis with algae, position of the gonopores, morphology of the bursal nozzles, lack of central singlet microtubules in the axonemes of spermatozoa, and funnel-like posture of the anterior end. Based on morphology and the results of molecular phylogenetic analyses, we assign this species to the genus Amphiscolops. Interestingly, these worms show unique behaviors such as swimming by flapping the lateral sides and actively capturing prey by swinging the anterior funnel. Furthermore, they possess a dorsal appendage—a characteristic previously unreported in Xenacoelomorpha—representing an evolutionary novelty acquired by this species.

The dynamics of microscopic marine plankton in coastal areas is a fundamental theme in marine biodiversity research, but studies have been limited because the only available methodology was collection of plankton using plankton-nets and microscopic observation. In recent years, environmental DNA (eDNA) analysis has exhibited potential for conducting comprehensive surveys of marine plankton diversity in water at fixed points and depths in the ocean. However, few studies have examined how eDNA analysis reflects the actual distribution and dynamics of organisms in the field, and further investigation is needed to determine whether it can detect distinct differences in plankton density in the field. To address this, we analyzed eDNA in seawater samples collected at 1 km intervals at three depths over a linear distance of approximately 3.0 km in the Seto Inland Sea. The survey area included a location with a high density of Acoela (Praesagittifera naikaiensis). However, the eDNA signal for this was little to none, and its presence would not have been noticed if we did not have this information beforehand. Meanwhile, eDNA analysis enabled us to confirm the presence of a species of Placozoa that was previously undiscovered in the area. In summary, our results suggest that the number of sequence reads generated from eDNA samples in our project was not sufficient to predict the density of a particular species. However, eDNA can be useful for detecting organisms that have been overlooked using other methods.