populations of Carassius auratus gibelio lived in Fangzheng County (Heilongjiang Province), Pengze County (Jiangxi Province) and Qihe River (Henan Province) were analyzed by RAPD method using twenty arbitrary primers. The experiment shows that fourteen primers were effective, each primer gave 2 - 13 bands for the each individual. The length of the fragment was 300 - 4000bp. According to the patterns, genetic variations of inter-and intrapopulations of C. auratus gibelio were analysed. Among three populations, the differences of fingerprints obtained by primers OPV - 07, OPV - 14 and OPV - 20 were so obviously that might be used to be molecular markers.