From 1995 to 2019, marine algae were sampled in the intertidal and upper subtidal zones of Amakusa Archipelago (Shimoshima Islands) and the southern islands of the Ryukyu Archipelago (Okinawa, Sesoko, Iejima, Akajima, Miyako, Ishigaki, Iriomote and Yonaguni). A total of 569 species and taxonomic forms of benthic macroalgaewere identified, of which 57% belonged to red algae, 15%belonged to brown and 28% belonged to green algae. On these islands, 153 taxa were found for the first time. During the period, the benthic marine flora of the individual islands has been studied with varying degrees of care.The most thoroughly studied island in the Amakusa group was Shimoshima (14 localities during all seasons) and in the Ryukyu Archipelago was Sesoko Island (8 localities in all seasons). The comparison of taxonomic and biogeographic characteristics of the marine floras of these two archipelagos: biodiversity of species and forms, taxonomic composition of algal communities, potential capabilities of geographic (latitudinal) distribution of taxa give us the basisto classify the benthic flora of Shimoshima Island as awarm temperate region of the Northern hemisphere in East Asia, and the southern islands of the Ryukyu Archipelago as a tropical biogeographic region.