Abstract: The objective of this study was to analyze conservation priorities of genetic diversity in Chinese indigenous duck breeds, and to supply a theoretical basis for better conservation programs. The DR genetic distance, gene flow, heterozygosity and polymorphism information content were measured by 28 microsatellite markers. Two conservation strategies, Weitzman and Caballero methods were used to assessed the conservation priorities of 24 Chinese indigenous duck breeds. The results showed that all the loci were neutral by Ewens-Watterson test, the mean PIC was 0.494 4. The SS and DY breeds respectively had the highest (0.864 8) and the least (0.720 8) observed heterozygosity. The JXD and JD breeds respectively had the highest (0581 6) and the least (0.434 7) PIC. SC breeds had the farthest mean genetic distance (0.425 7) and the least gene flow (0.471 1) with HZ breeds, XL breeds had the nearest mean genetic distance (0.166 4) and the most gene flow (1.380 8) with JXD. The Weitzman method suggested that the most important breeds to be preserved are LW, SC, GY and BJ, their contribution rate to diversity were higher than 5％. The Caballero method suggested that SX, SC, CH and XY breeds had higher positive contributions to total diversity. The priority order of Caballero method had some difference from that of Weitzman,s. The reason was that the Weitzman method did not take into account the withinpopulation genetic diversity. The full consideration to interpopulations genetic diversity and genetic diversity within populations should be given in the analysis of Chinese indigenous duck resources conservation levels. Sixteen breeds, including SX, SC, CH, XY, GY, LW, HZ, MY, JJ, SS, ES, BJ, HN, YN, YX and WS had higher contributions to overall genetic diversity of Chinese indigenous duck breeds, and should be given preferential protection levels.