We studied the variations in composition and species richness of trees in 24 plots from southern Kyushu to the northern Ryukyu Archipelago, Japan. Cluster analysis based on Jaccard index identified three forest zones: cool-temperate mixed conifer-broadleaf forest (MF), warm-temperate evergreen broadleaf forest (EBF), both north of the Tokara Gap (Kyushu and Yakushima), and subtropical EBF south of the Tokara Gap (Amami-Oshima, Tokunoshima and Okinawajima). The MF zone corresponded to Kira’s Warmth Index (WI) < 100℃. The boundary between the two EBF zones was determined by geohistory, not by climate (WI). Plot-level species richness per 400 stems increased with increasing WI, with decreased values in Yakushima, suggesting that geohistory (isolations from Kyushu and by the Tokara Gap) depressed the species richness of Yakushima. Greater species richness in the subtropical EBF was explained by the presence of species whose distributions were restricted to the south of the Tokara Gap. By contrast, lower species richness of MF in Yakushima than in Kyushu was due to the absence of species whose distributions were restricted to Kyushu northward. In conclusion, climate and geohistory jointly shape the tree-community composition and diversity of old-growth forests in this transitional zone from temperate to subtropical regions.