In the Ryukyu Archipelago, Japan, mangrove ecosystem is one of the major ecosystems around coastal region. In order to maintain the community, keeping habitat condition for regeneration is important. Muddy and soft soil, which supports mangrove seeds to stick easily, is needed for initial stage of their regeneration, and it is located at where sediment of bar surface is frequently exchanged during the flood. Present study focuses on the eco-hydraulic condition of Okukubi River, in Okinawa, southwestern Japan, and clarified the relationship between density of mangrove species and i) soil penetration and ii) absolute bed-level fluctuation (ABLF) during a flood which was estimated by simulation model of two-dimensional bed deformation analysis. As a result, i) the density of Kandelia mangal, pioneer species, negatively correlates with soil penetration in all stages. Regarding Bruguiera mangal, it shows negative correlation in maturing stage, and positive in matured stage. ii) The density of K. mangal and maturing tree of B. mangal negatively correlates with ABLF. While the density of maturing tree of B. mangal positively correlates with ABLF. It is consider that regeneration of the mangrove community is assisted by soft soil and its condition is formed by frequent exchange of sediment of river-bed surface.