We identified 40 genera and 83 species of scleractinian corals from middle Pleistocene reef limestones on Irabu-jima, located in the South Ryukyu Islands (South Ryukyus); these data were then combined with previously published data sets on Pleistocene coral assemblages on Okinawa-jima (southern Central Ryukyus), and Kikai-jima (northern Central Ryukyus) to perform statistical analyses, including cluster analysis and multidimensional scaling (MDS) ordination of Bray–Curtis (BC) similarity coefficients applied to coral taxa (R-type analysis) and coral assemblages (Q-type analysis). Results of the analyses, combined with field descriptions of the coral assemblages, allowed interpretations of reef paleoenvironments. Outcrops of Quaternary reef deposits in the Ryukyus comprise both shallow- and deep-water coral assemblages. Generally, coral diversity increases southward along the island chain. The statistical analyses highlight differences in the taxonomic compositions of fossil coral assemblages in different geographic areas and in distinct reef environments. We report on the differences among assemblages on Irabu-jima, Okinawa-jima, and Kikai-jima. Upper reef slope coral assemblages on Irabu-jima, which are similar to those on Okinawa-jima, are dominated by acroporid corals, mainly Isopora palifera and branching Acropora spp., encrusting to platy Porites spp., and branching Pocilloporidae. Porites spp. and faviids, such as Cyphastrea spp. and Favia pallida gr., are more typical of the upper reef slope on Kikai-jima. Lower reef slope assemblages on Irabu-jima are dominated by thin laminar colonies of Porites and/or Montipora species. Associated coral taxa are Stylocoeniella sp., Leptoseris spp., small fungiid corals, Trachyphyllia geoffroyi, and Montastrea valenciennesi. Data from two large outcrops on Irabu-jima highlight the relatively large spatial homogeneity of community structures in lower reef slope coral assemblages as compared with their upper reef slope counterparts.