Microsatellite-centromere recombination rates were estimated at 21 loci in relation to centromere of chromosomes in gynogenetic diploid lines induced from loaches of two different populations in Japan. All the microsatellite loci gave allelic segregation according to the Mendelian manner of inheritance in normal diploid families. Since loaches from Kita population in the southern area of Hokkaido Island and those from Memanbetsu population in the northern area, Hokkaido, Japan, were reported to be genetically diversified by previous genetic studies, map distances were compared between loaches from the two different populations. Three (Mado7, Mac3 and Mac49) of five loci, which could be compared inter-populationally, gave significantly different recombination rates, i.e., map distances. The results support the presence of genetic difference between the two populations.