Goats are an important domestic animal for animal husbandry that has attracted considerable research attention worldwide. Genetic diversity assessment and population genetic structure of indigenous goats can provide valuable conservation strategies. The current study aimed to evaluate the genetic diversity and population structure of six goat populations from Chongqing, China. A total of 145 animals from five local goat populations, namely, Youzhou black (UZG), Jianzhou (JZG), Banjiao (BJG), Dazu (DZG) and Hechuan white goat (HCG) and an introduced breed called Nubia goat (NBG) located in Chongqing, China were genotyped with 18 autosomal microsatellite markers. A series of genetic diversity parameters and population phylogeny were estimated and constructed. This study preliminarily showed that the six goat populations present rich genetic diversity and significant genetic divergence among them. Furthermore, material exchanges were observed between the introduced and local goat populations in Chongqing. This result will further explain the diversity conservation of Chongqing goat populations.