Abstract: Genetic heterogeneity and molecular markers were analyzed in two artificial gynogenetic populations of Red-white ornamental carp (Cyprinus carpio L.) by RAPD technique, using 30 10-nucleotide primers. Similar banding patterns were observed among individuals within each gynogenetic population, whereas obvious differences were detected between the two gynogenetic populations. 7 primers, such as Opo-7, Opo-9, Opo-12, Opo-14, Opj-4, Opj-8 and Opj-10 were observed to produce specific bands, and these bands could be used as molecular markers for discriminating the two different gynogenetic populations. Average genetic distances within and among the two populations clearly indicated their origin and relationship. Aphylogenetic tree was constructed using UPGMA cluster analysis based on a total of 1710 distinguishable fragments (171 per individual). All individuals in the first gynogenetic population were clustered into one group, while all the individuals originated from the second were joined into another group.