Abstract: The labeling effect of plumage color trait of mule duck were studied by RAPD and AFLP techniques.Theresults indicated that:①The bands were less in RAPD method, 297 clear bands were amplified by 37 primers in all.On average,4 bands were amplified from a primer.In total 37 primers,only 15 specific bands were obtained by 7 primers, thereinto 10 specific bands belonged to white-plumage mule buck.②AFLP fluorescent map was clear and bands were abundant ,more than 1000 bands were amplified by 16 primers combinations.In 16 primers combinations, 90 specific bands were obtained by 4 primers combinations, in which 37 specific bands belonged to whiteplumage mule buck.AFLP technique was more suitable to be used in studying plumage color trait in mule duck.