Traditional agro-ecosystems have sustained diverse aquatic plants, but have been greatly damaged by modern agricultural practices. Ottelia alismoides is a submerged macrophyte occurring in and around paddy fields, and a vulnerable species in Japan. Using four primer pairs of amplified fragment length polymorphism (AFLP) markers, genetic variation was estimated in 12 O. alismoides populations from Honshu, Shikoku and Kyushu. O. alismoides demonstrated low intra-population genetic variation (Pp = 15.7%, H-E = 0.052 and I = 0.080), which was explained by its annual life history, high level of autogamy and repeated genetic bottlenecks. These factors, combined with limited gene flows (Nm = 0.113-0.127, M = 0.091), also resulted in the high genetic differentiation among populations, contributing about 70% of the total genetic variation. The gene flow might be hindered by geographic distance, mountains within islands and the strait between islands. It is, therefore, recommended that conservation of all extant populations be prioritized to maximize gene representation
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