The subgenus Rhoicosphenula Lange-Bert. has a unique character combination that differentiates it from Gomphosphenia subgen. Gomphosphenia Lange-Bert. In particular, Rhoicosphenula has striae/areola features that are similar to Gomphosphenia, but is differentiated from that genus by also having pseudosepta present on both poles of the valves, copulae with septa at one of the poles, and frustules almost rectangular in girdle view. Together, this character combination strongly supports it as an independent genus following modern diatom-taxonomy criteria. Moreover, the only species of Rhoicosphenula known so far was collected from a peculiar acidic and dystrophic habitat, whilst most Gomphosphenia s.s. species colonize medium-conductivity, alkaline inland waters. On the basis of LM and SEM studies, we also propose a species of Gomphosphenia (G. patrickiana Cantonati, Lange-Bert., Kociolek & A.A.Saber, sp. nov.) as new to science. The new species is mainly defined by its valve outline and dimensions, length to breadth ratio, striation density, and geographical distribution. It was found in several samples of two streams in Puerto Rico, sometimes with high relative abundance. Gomphosphenia patrickiana Cantonati, Lange-Bert., Kociolek & A.A.Saber, sp. nov. was much more abundant in the stream with lower nutrient (in particular P) concentrations, and higher ecological integrity. The new species seems to prefer moderately alkaline freshwater habitats with medium-high conductivity and oligo- to mesotrophic conditions, with moderate tolerance to N enrichment. Also noteworthy is the occurrence of the new species in streams with above-average magnesium concentrations (due to the local geology). This Neotropical, warm-water species might be a potential indicator of global warming effects.