Neocaridina denticulata (Decapoda: Atyidae) is a freshwater shrimp with a land-locked life-history and is widely distributed in western Japan. The taxonomic confusion of this species, caused by the loss of type specimens, unknown type locality, and genetic and morphological geographical variation, has led to inconveniences in biodiversity conservation and the identification of exotic species that recently invaded Japan. Therefore, it is important to clarify this species’ distributional range and regional genetic and morphological characteristics to solve the problem. Here we report the first record of N. denticulata from Fukue-jima Island in the Goto Islands, Nagasaki Prefecture, Japan. Morphological analyses identified the population as N. denticulata, and mitochondrial DNA-based analyses suggested that the population was distinctly differentiated from the Kyushu populations. This population is essential for inferring the N. denticulata distribution formation and biota formation processes in the Goto Islands. On Fukue-jima Island, N. denticulata has only been found in one pond; thus, the Fukue-jima population is likely to be in critical condition.