Using a non-invasive method, 113 fecal samples from the Asian elephant population in Puer were collected. After getting total DNA using kits, specific amplification by 9 microsatellite loci resulted in a 49 unique genotypes which were identified by CERVUS 3.0. The analysis of genetic diversity through GenAlEx v6.5 and Arlequin v3.5 showed that loci didid not deviate from Hardy-Weinberg equilibrium; the average allele number was 3.111; the average Shannon's Information Index was 0.804; the average expected heterozygosity was 0.468and the average observed heterogosity was 0.476. Comparisons of genetic heterozygosity from different areas showed that the genetic diversity of Asian elephant in Puer was low.