Some fundamental natural-history traits of the endangered mud snail Cerithidea rhizophorarum were investigated for three years in an open, bare, sandy tidal flat located on the east of Shikoku Island in southwestern Japan. Our study demonstrated a highly aggregated distribution of younger snails and complicated differences in vertical migration patterns between younger and older snails that might have prevented comprehensive understanding of the precise demography of C. rhizophorarum in previous studies. From late summer, juveniles of the first-year cohorts appeared patchily at 12–16 cm lower tidal heights than snails of the oldest cohorts and reached 5.0–7.5 mm in mean shell length by the first mid-autumn. In the second year, juveniles gradually moved upward and appeared at higher tidal heights. The second-year cohorts reached 15.6–19.1 mm in mean shell length by the end of the second autumn and converged into the oldest cohorts during the third year or later. Our results suggest that C. rhizophorarum matures sexually and starts reproduction from the fourth summer at the earliest. On the other hand, older snails showed a similar seasonal migration pattern every year—downward movement in summer and upward movement in autumn—probably associated with their reproductive activity and/or a seasonal change in the maximum tidal height. For conservation of C. rhizophorarum, it is very important to preserve both the higher area as a main habitat for older snails and the lower tidal flat as the nursery ground.