The present study investigated the distribution of Batillaria multiformis and B. attramentaria in the tidal flats of Southern Kyushu. These two species are the dominant inhabitants of tidal flats and play an important role in conserving the environmental condition of the coastal area. Since it is difficult to distinguish between the two species based on shell morphology, the polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) technique was used for identification. Among the 55 tidal flats surveyed, Batillaria species were found in 32, mainly along the coasts of Kagoshima Bay and East China Sea. Furthermore, these species were not observed in certain tidal flats, although their presence in these tidal flats was confirmed from 1999 to 2003. The reason for their absence or decline has been discussed here. Batillaria multiformis was distributed along the neighboring tidal flats of inner Kagoshima Bay and around Nagashima Island, whereas B. attramentaria was isolated along a few scattered tidal flats facing to the Pacific Ocean or East China Sea. The difference in the distribution of two species might be attributed to their developmental system—B. multiformis and B. attramentaria employ planktonic and direct developmental systems, respectively.