The Ryukyu Islands have experienced a complex history of island connection and separation since the Late Miocene. Questions persist regarding how organisms have evolved through changes in island configurations over millions of years particularly in the Central Ryukyus, which is characterized by high species endemism. We conducted comparative phylogenetic and phylogeographic analyses among island populations targeting five mammalian species (Pentalagus furnessi, Diplothrix legata, and three Tokudaia species), all of which belong to genera endemic to the Central Ryukyus, employing genome-wide SNP and mitochondrial DNA variation analyses. The SNP and mitochondrial DNA analyses across these genera revealed distinct lineages on each island (Amami-Ohshima, Tokunoshima, and Okinawajima, except for P. furnessi absent from Okinawajima), with the Amami-Ohshima population showing the highest genetic diversity. Divergence times between island populations were estimated to be in the Middle Pleistocene for P. furnessi and D. legata and ranged from the Late Miocene to the Early Pleistocene for Tokudaia. These findings, along with those of previous studies on other terrestrial animals, emphasize the significant impact of pre-Pleistocene island isolation on genetic divergence in species with limited dispersal abilities, while some species exhibited inter-island migration by the Middle Pleistocene.