The objective of this research was to investigate the influence of chicken genotype on various eggshell traits, egg quality, and ultrastructure during the egg production phase. Five established chicken strains, Fayoumi black, Fayoumi red, Fayoumi white, naked neck (Na) white, and Na red, as compared with commercial layer brown chickens were examined in this study. A total of 60 eggs from each genotype were used to determine egg quality and eggshell ultrastructural. The results of this study indicated that the genotype had a significant impact on various parameters including egg weight, egg length, egg width, shape index, albumen height, albumen weight, albumen percentage, yolk height, yolk diameter, yolk index, yolk weight, yolk percentage, yolk albumen ratio, wet shell weight, dry shell weight, and shell percentage. Specifically, the naked neck strain eggshell exhibited distinct ultrastructure defects such as late fusion, poor confluence, and different striations compared to the Fayoumi strain and commercial eggshell. On the other hand, the Fayoumi eggshell showed favorable ultrastructure features like early fusion and cuffing compared to the Na strain eggshell. These findings suggest that genetic differences among layer strains can significantly impact egg quality. Therefore, it is important to consider genotype when evaluating eggshell traits, egg quality, and ultrastructure. By understanding these genetic variances, improvements can be made to the overall performance and quality of eggs in egg production systems.