Nucleotide sequences from the control region of the mitochondrial (mt) DNA were analyzed for Japanese loggerhead turtles (Caretta caretta) to elucidate population genetic structure and phylogeography. Three haplotypes were detected among 259 females sampled from four nesting sites in 1994-1999. Within nesting colonies, haplotype frequencies were not significantly different between sampling years, whereas among nesting colonies, they were significantly different and fixation indices (F-st) were significantly >0 in most comparisons. These findings indicate that nesting colonies of Japanese loggerheads are genetically distinct and that Japanese females show precise natal homing on an ecological time scale. There were no obvious latitudinal variations in the mtDNA diversity among Japanese nesting populations in contrast with those of the USA, where a series of colonization bottlenecks on northern nesting populations accompanied by postglacial expansion are supposed to be the cause of the trend. Since (1) the mtDNA diversity of Pacific loggerheads consists of a small number of divergent haplotypes and (2) their population size is smaller than those of loggerheads inhabiting other regions, the Pacific loggerheads might have experienced more critical bottlenecks than the others. The discovery of a female with the haplotype that had previously been detected in the nesting colonies of the South Pacific but not the North Pacific made us reconsider the stock composition of loggerheads observed in the North Pacific; that is, all loggerheads inhabiting the North Pacific are derived from Japanese beaches.