Local chicken breeds play vital roles in rural development and sustainability; therefore, the preservation of local breeds’ genetic diversity is crucial, also, assessing and advancing local breeds is crucial considering the impact of climate change on chicken production. The current study evaluated the differences between a fully feathered local chicken line (CE2) and a naked-neck local chicken line (CE4) at the microsatellite loci level. For this purpose, nine microsatellite primers were used to scan the genomes of both lines. The results generated by different loci between the two lines showed that the lowest allele numbers were 0 and 4 alleles detected at loci LEI0094 and MCW217, respectively, and the highest allele number was 10 detected at MCW328 and ADL299 loci, with an overall mean of 6.69 alleles/locus. The levels of heterozygosity were relatively high and were higher for line CE4 than for line CE2. The genetic distance between males and females of line CE2 was shorter (0.018) than that between males and females of line CE4 (0.104), and the opposite was observed for genetic identity. Also, ΦPT values were 0.088 (P<0.001), and 0.080 (P<0.01) for line CE2 and line CE4, respectively. The association between alleles and body weights revealed different alleles of microsatellites MCW217, MCW328, MCW193, ADL299, and MCW064 contributed significantly to body weight variance at different ages. The study provided an outlook on the genetic diversity of two chicken lines and indicated substantial room for improvement within Egyptian native breeds. تفاصيل المقالة