In the present study, microsatellite DNA was isolated and enriched from the genomes of Channa argus and C.maculate by magnetic beads. Sixty-two pairs of microsatellite primers of C.argus and C.maculate were designed based on the flanking sequence of the microsatellite loci with software Primer 3.0 or Primer 5.0.Ten primer pairs failed to amplify. Among the 52 primer pairs which could effectively amplify products, 49 universal primer pairs could effectively amplify in F1 generation. Loci CHA16 showed monomorphic in C.maculate and polymorphic in C.argus and loci CHM23 was opposite. In addition, CHM24 showed monomorphic in C.argus and failed to show in C.maculae. Moreover, 22 specific loci between C.argus and C.maculate were screened out, and 18 specific loci could identify C.argus , C.maculate and the reciprocal hybrids alone effectively. Combination of the other 4 specific loci also effectively identified C.argus , C.maculate and the reciprocal hybrids. However, the reciprocal hybrids [C.argus (♀)× C.maculata (♂), C.maculata (♀)× C.argus (♂)]could not be identified in this research.