The present study investigated the species composition of freshwater shrimp fauna in Kikai-jima Island within the Ryukyu Islands in southern Japan. Six stream-pool sites, with Karimata-no-izumi in the north, followed by Shiomichi, Nagamine, Ooasato, Takigawa, and Urabaru, were sampled from June 2005 to June 2008. We identified eleven species belonging to two families: four Palaemonidae, and seven Atyidae. The most dominant species were Caridina typus as well as C. sakishimensis, which is a redlist (RDB) species sporadically distributed in the Ryukyu Islands. Together with C. typus and C. sakishimensis, M. lar and M. japonicum also dominated most of the study sites in Kikai-jima, and Morista's similarity index showed high similarities between five of the stations, except for Takigawa in the south. The highest densities of shrimp were recorded in Karimata-no-izumi followed by Ooasato, Nagamine, Urabaru at the southernmost, Shiomichi, and Takigawa. Comparing species composition in Kikai-jima and other islands of the Ryukyu group, cluster analyses showed greatest faunal similarity to Kume-jima in the lower central Ryukyus, with the Redlist C. sakishimensis recorded in both islands. This close similarity in shrimp composition between the two distant islands may be attributed to their geological origin and sizes of the islands, both measuring about 60 km² in area.