Rapid adaptation and speciation have not been well documented for organisms in Lake Biwa, Japan, the oldest ancient lake in East Asia. To examine these processes, we focused on the divergence of Sarcocheilichthys gudgeons and conducted phylogeographic and population genetic analyses using mitochondrial DNA sequences and microsatellite data. No remarkable genetic differentiation was found between two species, S. biwaensis and S. variegatus microoculus, both endemic to Lake Biwa, whereas this species group, including S. v. variegatus, was genetically divided into three major regional groups: the Lake Biwa, Ise Bay, and western groups. Divergent mtDNA haplotypes were included within the Lake Biwa and western groups, strongly suggesting secondary contacts among allopatrically isolated populations. Dating for mtDNA phylogeny using a geological constraint suggested the colonization of Lake Biwa by multiple Sarcocheilichthys lineages that diverged from each other in the early-middle Pleistocene. Coalescent-based population analyses indicated that the local populations colonized the rocky bottom habitat in Lake Biwa from other habitats after the Last Glacial Maximum, likely reflecting past environmental changes in the lake, including the disappearance of rocky areas during the glacial climate. Divergent morphological adaptation in Sarcocheilichthys associated with substrate type may have rapidly proceeded along with environmental changes. Keywords Ancient lake • Central Japan • Gobioninae • Historical demography • Phylogeography • Trophic polymorphism (73%) haplotype (Fig. 2). A subclade of clade A, consisting of A15 and A16, and a tip haplotype, A18, were detected exclusively from the Chugoku region. Clade B haplotypes were obtained from the Lake Biwa, Kinki, and Chugoku regions, but showed some regional distribution patterns. The most interior haplotype of clade C (C03) was exclusively found in Kyushu, but the tip haplotypes were shared by specimens from the Lake Biwa, Kinki, and Chugoku regions. Clade D was endemic to the Yura River system (Kinki), and clade E was the earliest divergent group and was endemic to the Ise Bay area (Figs. 2, 3). Node tMRCA*(mean*±*SE) 95%*HPD