Abstract: Genetic diversity and relationships of Grass goldfish，Red dragoneye goldfish，Red-head wen goldfish，Blisters-eye goldfish，White-head oval goldfish using RAPD technique was analysed. A total of 116 loci，including 27 polymorphic ones，were detected from the five populations by using 14 primers.The average percentage of polymorphic loci to total DNA of the five populations was 23.3% .The results showed that the genetic similarity index of the five varieties of goldfish ranged between 0.818 and 0.8759 which was lowest (0.8759) between Grass goldfish and Red dragoneye goldfish,and their genetic distance was the highest(0.1241) that indicated the phylogenetic relationship was far; Red-head wen goldfish and White-head oval goldfish that the genetic similarity index was highest(0.9182) and the genetic distance was lowest(0.0818) was closer. Clustering analysis by both UPGMA method and NJ method showed that the phylogenetic relationship between Grass goldfish and Red dragoneye goldfish was quite near, as well as Red-head wen goldfish and White-head oval goldfish was near. These considerably are consistent with the evolutionary positions among these fishes. Both results were accordant.It`s important to study the genetic diversity of goldfish on its quality protection.