The genome of Litopenaeus vannamei was analyzed by random amplified polymorphic DNA (RAPD) analysis to identify DNA markers for important traits in Litopenaeus vannamei in the South China. A total of 20 ten-bases primers were screened, and eight positive primers giving highly reproducible RAPD patterns were selected for comparison between healthy and diseased populations of Litopenaeus vannamei. A total of 38 reproducible RAPD fragments ranging from 200 to 1750 base pairs were scored, and 24 fragments (62.2%) were polymorphic. Only three RAPD markers, OPX-01-1020, OPX-14-530 and OPX-17-940, were found in the diseased population of Litopenaeus vannamei, suggesting the potential use of them as DNA markers for helping broodstock management and selection for breeding.