The population genetics of Anopheles sinensis, a major malaria vector in South Korea, was studied based on the nucleotide sequences of a 238-bp variable region of the mitochondrial control region. Three features of genetic variance were observed. First, the Taebaek and Sobaek mountain ranges may function as genetic barriers between the Northern Group (NG) and the Southern Group (SG). These mountain ranges are associated with the subdivision of the population, and significant and unique population differentiation was observed in the examined area. Second, the genetic cohesiveness observed within each group may have been caused by a recent expansion in the population rather than recurrent gene flow. Third, a marked dissimilarity in the genetic diversity between the two groups may also have resulted from several factors that caused a difference in the effective population sizes.