Abstract: Random Amplified Polymorphic DNA (RAPD) analysis was used with 10 primers to assess genetic variability in Shanxi native goats (Yangcheng White，Licheng Daqing，Lüliang Black). The results showed as follows: 1.The DNA of 3 breeds provided a great number of molecular markers with high polymorphism. 2. According to their RAPD fingerprinting map, the genetic distance and average band similarity among 3 breeds were calculated, 0.182 7 between Yangcheng White Goat and Licheng Daqing Goat is the smallest. Cluster analysis also showed that Licheng Daqing Goat and Yangcheng White Goat from alike region had a smaller distance. 3. The genetic diversity and its partition within and between populations of the 3 populations were calculated by using Shannon index. The genetic diversity index of Licheng Daqing，Yangcheng White，Lüliang Black were 0.328 8，0.349 9 and 0.154 5 respectively, Genetic differentiation (Gst) was estimated to be about 68.49% among 3 populations. The results indicated that the genetic variation was mainly among breeds; the genetic character of Lüliang Black Goat was peculiar in native breeds indicating that protection and further selection should be strengthened.