The aim of this study was to compare the genetic variation of three developed chicken strains (Matrouh, El-Salam and Bandarah). Nine highly polymorphic microsatellite markers were used in 133 birds. One hundred fifteen alleles were detected in the overall populations with a mean number of 12.78 alleles per locus. The highest number of alleles was 24 for microsatellite marker MCW 49. While,  ADL171 and MCW 43 loci recorded lowest number of alleles across all populations (8). Dendrogram was generated from estimates of genetic distance among chicken populations. Mean number of alleles per strains overall loci ranged from 4.00 for Bandarah to 4.44 for Matrouh. Number of specific alleles was 8 for all strains studied and effective number of allele (ENA) ranged from 1.49 for MCW43 to 4.95 for MCW49.  Averages of expected heterozygosity (H_E) were 0.597, 0.601 and 0.607 for Matrouh, El-Salam and Bandarah chicken populations, respectively. Dendogram Based Nei's genetic distance revealed that Matrouh and Bandarah chicken populations are closely related than that of El-Salam .The study revealed the existence of moderate genetic diversity in chicken populations studied and also showed that the markers used were highly informative and can be used in future studies involving breeding, management and conservation of chicken populations.