Abstract: Twelve microsatellite markers from Silurus meriaionalis were selected to analyze the application on fourclosely related species of siluriformes including S. meriaionalis, S. lanzhouensis, S. asotus and C. fuscus. Among thetwelve microsatellite markers, eight microsatellite loci had high versatility, and the number of alleles per locus rangedfrom 2 to 15. The loci with AC repeat motif had more allele, on which the polymorphisms were higher than others. Theother four loci either had no specific amplification bands (DQ223147 and DQ223160), or no polymorphism (DQ223149and DQ223159). The average value of observed heterezygosity (Ho) was 0.7571; the average of expected heterezygosity(He) was 0.6870; and the polymorphism information content (PIC) was 0.6441. Taken together, the values indicated theeight locis were highly polymorphic, therefore suitable for siluriformes genetics research. In addition, phylogenetic treeconstructed by Nei’s-genetics distance divided four species of siluriformes into two groups, one included S. lanzhouensisand S. asotus, the other contained S. meriaionalis and C. fuscus. Three rare genotype-specific locis (DQ223146,DQ223151 and DQ223173), among 8 effective locis, could be employed to identify the 4 species of siluriformes.Therefore, they add density of genetic markers on genetic linkage map. More important, it would construct solid foundationfor siluriformes germplasms protection and molecular breeding.