Batesian mimicry is a striking example of Darwinian evolution, in which a mimetic species resembles toxic or unpalatable model species, thereby, receiving protection from predators. In some species exhibiting Batesian mimicry, non-mimetic individuals coexist in the same population despite the benefits of mimicry, and the relative abundance of mimetic individuals in the population varies among localities. In a previous study, we found that the mimic ratios (MRs), which varied among the Islands, were likely to be explained by the model abundance of each habitat, rather than isolation-by-distance or phylogenetic constraint in the swallowtail butterfly, Papilio polytes, on the Ryukyu Islands in Japan. Because the previous study, however, was based on the mitochondrial DNA (mtDNA) that may sometimes mislead conclusion stemming from the inherent genetic properties, this possibility was reexamined based on hundreds of nuclear single-nucleotide polymorphisms (SNPs) of 95 P. polytes individuals from five Islands of the Ryukyus. We found that the population genetic and phylogenetic structures of P. polytes largely corresponded to the geographic arrangement of the habitat Islands, and the genetic distances among island populations significantly correlated with the geographic distances, which was not evident by the mtDNA-based analysis. The revised SNP-based genetic distances with a partial correlation approach revealed that the MRs of P. polytes were strongly correlated with the model abundance of each island, implying that negative frequency-dependent selection shaped and maintained the mimetic polymorphism. Taken together, we suggest that predation pressure, not neutral factors, is major driving force to determine the relative abundance of Batesian mimicry in P. polytes from the Ryukyus.