A high level of geographical variation at an exceptionally fine scale was detected in the mitochondrial 16S ribosomal RNA genes of a land snail species Euhadraquaesita from the Kanto region of Japan. In total, 50 haplotypes were detected from 27 populations, with most sample sites possessing private alleles. In some individual populations the different haplotypes do not fall as a monophyletic group, so that some of the haplotypes are phylogenetically distant, differing from each other by > 10%. In contrast, phylogenetically similar haplotypes were found in separate sites at long distances from their main distribution. Together, these findings strongly suggest that contraction and expansion of populations has occurred repeatedly in the past. The subsequent expansion of populations and migration from different areas may have mixed distant populations. This repetition of isolation and mixing has resulted in an exceptionally fine scale of geographical variation, and the accumulation of high genetic diversity within and between populations of this species.