This study analyzed genetic diversity in indigenous chicken populations from Iraq. Fifty-six samples were collected from four locations and sequenced to identify mitochondrial DNA haplogroups. Eleven haplotypes belonging to three haplogroups were found. Haplogroup D was most common, seen in 50 chickens, while haplogroups A and B occurred at low frequencies. Genetic diversity varied between locations. The high frequency of haplogroup D supports an origin in the Indian subcontinent for Iraqi village chickens. Rare haplogroup B may result from recent introgression with commercial chickens, while haplogroup A could be linked to historical visitors rather than coastal trade.