Abstract: In order to investigate the genetic resources status of mainly goat breeds in tropical and subtropical region of China, the author detect the genetic diversity of Longlin goats and Leizhou goats which distributed different locations by 14 pairs Microsatellite primers. The result showed that the average polymorphic information content (PIC)of Longlin goat (Liuzhou and Baipeng) and Leizhou goat (Xuwen and Hainan) were 0.645, 0.600, 0.483, 0.518, average heterozygosity were 0.281, 0.421, 0121, 0.157 and average number of alleles were 5.17, 4.93, 4.64, 4.5 respectively, three sets of data indicated that the two goat breeds was lack of genetic diversity relatively and genetic variation was lower; the clustered result of NJ Methods showed that two groups of Longlin goats clustered into one category, then clustered with Leizhou goat (Xuwen) together, for the final was Leizhou goat (Hainan), This was in accordance with the origin and geographical distribution of two breeds, The results of this study provide the basis and scientific data for the goat breeds resources development and utilization in tropical and subtropical region of China.