According to Ohno [
19], half-sisters should inherit the same mitochondrial genome from their mothers, but within a certain period of time, their offspring can also establish an independent lineage due to the accumulation of mutations. Since the Darwinian era, the origin and domestication of domestic chickens have attracted attention in many disciplines. Many studies have been carried out on the maternal origin of domestic chickens using mtDNA sequences. These studies indicate that red jungle fowl are the original ancestors of domestic chickens [
20]. However, several independent domestication events occurred in southern China, South Asia, and Southeast Asia, possibly involving multiple maternal origins [
5,
21]. Liu et al [
5] analyzed mtDNA D-loop hypervariable regions in 834 chickens in Eurasia and 66 red jungle fowl in China and Southeast Asia and concluded that chickens originated on the Indian subcontinent and in southwestern China and its surrounding areas [
5]. Niu et al [
6] studied the phylogenetic relationships of six indigenous chickens in China and showed that the chickens descended from red jungle fowl in Thailand and its surrounding areas. Song et al [
22] reported that six native Chinese chickens closely related to
G. g. gallus,
G. g. jabouillei, and
G. g. spadiceus distributed in Yunnan Province and Laos may have originated from red jungle fowl subspecies in Yunnan, Laos, and Vietnam and its surrounding areas. Gong et al [
23] reported that Piao chickens have five maternal origins. In this study, the phylogenetic trees of the six indigenous chickens were mainly divided into two clusters (A and E), suggesting two major maternal origins (
Figure 1). The A and E haplogroups in this study correspond to the A and E haplogroups in the study of Liu et al [
5]. Haplogroups A and B are distributed throughout the world (except Africa), having originated in Yunnan or its surrounding areas, and haplogroup E is also widely distributed in the maternal pedigree, mainly having originating on the Indian subcontinent [
4,
5]. Based on these patterns, TP, HN, and HD chickens, which clustered into the A haplogroup, likely originated in Yunnan or surrounding areas, and BY chickens and commercial chickens, in the E haplogroup, mainly originated on the Indian subcontinent. JN and MQ chickens may have been distributed in both the A and E haplogroups due to gene flow.