The invention belongs to the genetics field and relates to a molecular genetics identification method for channel catfishes and flathead catfishes. The molecular genetics identification method for channel catfishes and flathead catfishes comprises the following steps: respectively extracting genome DNA (deoxyribonucleic acid) of to-be-identified channel catfishes and flathead catfishes; performing PCR (polymerase chain reaction) amplification on amicine genes of the channel catfishes and flathead catfishes; sequencing and comparing; if AGC microsatellites, starting from the 83th locus, of the MSTN (myostatin) gene are repeated for six times, identifying the catfishes as channel catfishes, and if the microsatellites are repeated for seven times, judging the catfishes as flathead catfishes. The molecular genetics identification method disclosed by the invention can be used for quickly, simply and conveniently, accurately and effectively identifying the channel catfishes and the flathead catfishes, is good in result stability and high in repetitive rate, so that the blank of identifying channel catfishes and flathead catfishes according to the existing domestic molecular biologic criteria is filled up.