Poultry production plays an important role as a source of cheap and high quality animal protein in Egypt. A 30 laying hens at 34 weeks age from each of Fayoumi, RIR and WL chicken breeds were evaluated for body weight and egg production traits. RIR recorded a significant heavier body weight while WL chickens recorded the highest and significant mean for egg number during the period of study. Fayoumi recorded the highest values for yolk index and yolk percentage. Fayoumi showed higher and significant values for most of the external egg quality characteristics compared to RIR and WL breeds. Blood samples were collected from the wing vein of 25 hens from each breed for DNA extraction and microsatellite genetic analysis. The highest value of expected heterozygosity (0.617) was obtained for Fayoumi breeds. The inbreeding coefficient (FIS) was ranged from 0.084 to 0.156 with an average 0.124. The neighbor-joining phylogenetic tree showed closer relation between Fayoumi and WL. The low production traits of Fayoumi breed might be improved by crossbreeding with exotic breeds such as RIR and WL chickens. We confirm the efficiency of microsatellites for genetic characterization of Egyptian chicken breeds.