Microsatellite analyses of sympatric populations of a tideland snail endemic to the Nansei Islands, Japan, Batillaria flectosiphonata, and its sister species, Batillaria multiformis, from a tideland on Amami-Oshima Island, indicated that the two species are reproductively isolated from each other, confirming the validity of B. flectosiphonata, whose monophyly was supported only by a low bootstrap probability in the previous molecular phylogenetic analysis. Egg capsules of B. flectosiphonata from Tokunoshima Island of the Amami insular group and Okinawajima Island of the Okinawa insular group were examined, which revealed that this species is a direct developer. Thus, the direct development has evolved twice within batillariids in Japanese waters. The lower genetic diversity of B. flectosiphonata than that of B. multiformis in the sympatric habitat might be attributed to its long-term isolation within the Amami insular group.