Seagrass habitats on coral reefs support unique fish assemblages. Accordingly, preservation of both coral areas and associated seagrass habitats is essential for maintaining high levels of biodiversity of coral reefs. This study aimed to clarify the fish assemblage structures in six extensive seagrass beds in the Sekisei Lagoon, viz. east of Iriomote Island, north of Kuro Island, east and west of Kohama Island and east and west of Taketomi Island, and determine which beds were most suitable for preservation, thereby conserving the resident fish species. Six combinations of the seagrass beds covered all of the seagrass-specific species, with the partial exception of Halichoeres melanurus. However, preservation of coral areas, where both juveniles and adults of that species are abundant, should suffice, thereby making each of the combinations tenable. However, the combinations including the seagrass bed north of Kuro Island supported relatively fewer fish individuals, therefore being less cost effective than the other combinations. In conclusion, in the case that not all of the seagrass beds are able to be preserved for some reason, a combination of those east of Iriomote Island, east and west of Kohama Island and west of Taketomi Island, or the alternative combination of those beds plus that east of Taketomi Island, should be preserved, in order to provide permanent habitats for the overall seagrass fish community.