Analysis of SNPs on the Z sex chromosome is thought to be a useful approach to estimate genetic diversity and genetic relationships in chicken populations. The objective of this research was to analyze the genetic diversity and genetic relationship of Indonesian native chicken populations. Here, we genotyped six unlinked SNP loci on the Z chromosome of 103 hens and 85 cocks from the four populations of Indonesian native chickens: Black Kedu (BK), Kedu (KD), Kampung (LOC), and Arab (AR). Genetic diversity and matrix pairwise distance FST were computed for 23 BK, 116 LOC, 20 AR, and 29 KD chickens. Average expected heterozygosity was greater in LOC and KD than BK and AR. The lowest pairwise FST value was estimated at 0.028 (P<0.05) between LOC and KD. In contrast, the pairwise FST value between BK and AR was larger (0.092) and was significant (P<0.05). These results suggested that LOC and KD are related closely, whereas BK and AR are related more distantly.