Aphyocypris chinensis has drastically decreased in Japan and has been designated as an endangered species. Using allozyme analysis, we tested the genetic diversity of A. chinensis strains maintained by five institutions in Japan for conservation purposes. Twelve loci encoding eight enzymes were scored. Alleles per locus ranged from 1 to 1.250, proportion of polyallelic loci was 0 to 0.250, and heterozygosity varied between 0 and 0.128. Genetic variations were found in the strains of three institutions, although no genetic variation was observed in the strains of the other two. Genetic diversity of a strain kept by the Hinamoroko Foster-parent Club was the highest, and even exceeded that of other freshwater fishes.