The present study aimed to conduct genetic diversity of four native chicken genotypes (Naked neck, frizzled, naked neck-frizzled and normally feathered). Diversity was assessed based on morphological measurements and molecular markers. A total of 500 chickens were used in this study. Productive traits of four genotypes were measured. RAPD technique was used to access the genetic diversity using five RAPD molecular markers. Main results referred to that naked neck and naked neck-frizzled genotypes had higher significantly body weight and body weight gain than normal feathering (nana-ff) ones. Naked neck-Frizzled (Nana-Ff) genotype had better carcass characteristics than other genotypes. Nana-Ff and Nana-ff genotypes were significantly higher than other genotypes in egg weight. The percentage of polymorphic bands ranged between 13.33 % and 40 % with a mean of 25.83 %. Genetic diversity ranged between 0.06 and 0.18 with a mean of 0.12. Constantly, the minimum values were scored to the genotype nana-Ff while the maximum values were scored to the genotype Nana-ff. Conclusion indicated that Na- allele is effective in improving meat and egg production traits than frizzle and normal feathering chicken. The Principal Component analysis in this study reflected that a similar results to that of the morphological values to four genetic groups. We provide fundamental evidence to genetic improvement programs by crossing or selection methods based on each productive performance and genetic analysis by modern techniques and software.