This study aimed at the evaluation of genetic variation in 5 different local chicken populations in Egypt. The populations were Fayoumi, Sinai Bedouin, White Baladi, normally-feathered Baladi (CE2) and naked-neck Baladi (CE4). Four microsatellite markers were used to screen the genomes of the chromosomes 3, 4 and 5 in the chicken populations. A total of 35 alleles were detected at the microsatellite loci, and averaged 8.75 alleles per locus. Sinai Bedouin fowl had a total of 19 alleles overall loci with an average of 4.75 alleles/locus, whereas Fayoumi, White Baladi, CE2 and CE4 had less total numbers of alleles with averages of 2.33, 2.75, 2.25 and 2.50 alleles/locus, respectively. Sinai Bedouin showed more allelic diversity than the other breeds. In addition, many alleles at many loci were population-specific, and Sinai Bedouin had the highest number of them, with a total of 10 alleles overall loci. White Baladi, CE2 and CE4 had a total of 2, 3 and 3 specific alleles, while Fayoumi did not have any. The genomic variability within populations was in general lowly moderate to moderate, with averages of 0.519, 0.447, 0.286, 0.417 and 0.542 in Fayoumi, Sinai Bedouin, White Baladi, CE2 and CE4, respectively. Sinai Bedouin showed the least percentage of allele similarity with all other populations with an average of 2.21%. Also, White Baladi and Fayoumi showed low allele similarity with other populations with percentages averaging 2.34 and 2.43%, respectively. The populations CE2 and CE4 showed the highest allele similarity with other populations with averages of 3.75 and 3.69%, respectively. The populations CE2 and CE4 shared an average 6.90% of the same alleles.