The aim of this work was to develop a strategy for using a genetic analysis for identifying native animals in regions where local breeds have been crossed with improved breeds and then compare that strategy to the overall morphology and breeding histories of the herds for identifying these animals.The experiment included the Chongrning white goat population, which is a crossbred of native animals with the Boer breed.Whole herds were assigned to Boer goat (42 animals), crossbred (60 animals) or Chongrning white goat (36animals) groups.High positive FIS showed that inbreeding existed in the subpopulations.The index of genetic differentiation, Neis standard genetic distance and Reynolds genetic distance were calculated and found to be significantly different between the three groups.The CM and BR groups were the most distant whereas the crossbred group was closer to the CM group.The proportion of the genome derived from two ancestral populations (native CM and BR) was assessed using the STRUCTURE software.Animals were assigned to three clusters on the basis of native Chongrning white thresholds.There do not have a good correspondence between the empirical (morphology and breeding histories) and the objective genetic analysis was found.It essential to establish core germplasm of Chongrning white goat by molecular maekers.