Abstract: The Nei’s improved genetic distance (DA) and gene flow (Nm) were measured using 16 microsatellite markers. Then two dendograms of clustering based on DA genetic distance using neighbor joining (NJ) method and Structure program were constructed to analyze the genetic structure and relationship among ten Chinese indigenous chicken breeds. The results showed, in dendograms of clustering based on DA genetic distance using NJ method, ten Chinese indigenous chicken breeds were divided into two main clusters, one was light weighted (including CHA, TIB, XIA, GUS and BAI), the other was heavy weighted (including LAN, DAG, YOU, LUY and XIS). In light weighted cluster, TIB and CHA, XIA and GUS were respectively clustered into one branch. In heavy weighted cluster, XIS and LUY were clustered into one branch, but LAN, DAG and YOU were clustered into independent branches. This result was consistent with Nm among ten chicken breeds. Structure program properly inferred the presence of genetic structure at the condition of not defining the origin of individuals. The genetic cluster inferred by Structure program was probably consistent with DA distance cluster method. However, Structure program determined the migrants and admixed individuals in ten chicken populations, which could not be found through DA distance cluster method.