This study was conducted to assess the population and genetic diversity of TNFRSF1A and zyxin genes among the Nigerian indigenous (Naked neck, Normal  and  Frizzle  feather) and Nera Black chickens (exotic chicken). Blood samples were collected from 400 chickens belonging to the genotypes described above and genomic DNA extracted using commercially available kit. Genomic regions containing zyxin and TNFRSF1A genes were amplified, sequenced and analyzed using Bioedit, DnaSP, MEGA and PANTHER software. The results from analysis revealed that Naked neck and Normal feather chickens had the highest mean value of nucleotide substitutions per sites (Dxy) (0.081), while Frizzle and Nera Black local chickens had the lowest Dxy value of 0.065 for TNFRSF1A gene sequences. The results from the analysis of zyxin gene sequence revealed that Frizzle and Normal feather chickens had the highest Dxy (0.6551), while Normal feather and Naked neck chickens had the lowest Dxy (0.0739). Nera Black chickens TNFRSF1A gene sequence had the highest mean values of haplotype diversity and average number of nucleotide difference (0.923 and 3.967 respectively). In zyxin sequences, the highest average number of nucleotide difference (3.143) and nucleotide diversity (0.00489) were detected in the Frizzle feather chicken. The analyses of these two genes sequences revealed high nucleotide divergence and haplotypes diversity. The results of divergence, haplotypes diversity and phylogenetic tree indicated a historically restricted gene flow among the genotypes.