Ten strains of Artemia parthenogenetica have been collected from inland salt lakes and coastal salterns in China. Ten diploid clones were selected from each Artemia parthenogenetica strain for analysis of the population genetic structure and genetic differentiation using inter simple sequence repeats (ISSR). One hundred and seventy fragments (100–2200 bp) were generated using 20 ISSR primers. A high level of genetic variation was found, with 96.47% polymorphic loci in total loci. The number of alleles (Na), effective number of alleles (Ne) and Shannon information index (SI), the mean Nei's gene diversity (H), the average values of Ht, Hs, Gst for pairwise subpopulations and mean value of all 100 clones from 10 Chinese Artemia parthenogenesis strains were analyzed. The results showed that genetic structure of populations of A. parthenogenetica from China were complicated with high genetic diversity among the populations. Cluster analysis was then performed to create a dendrogram using the UPGMA method based on the Nei' genetic identity. The UPGMA dendrogram showed that 10 Chinese Artemia parthenogenetica strains can be significantly divided into three major groups (subpopulation): Liaoning, (PK and YK); Shandong and Hebei, (HH, TG, LN, WD, WZ and FC) and Qinghai and Xinjiang (GH and BLK).