The genetic variation, structure and relationship of six Egyptian chicken strains including two Fayoumi selected-lines and four synthetic breeds (n=150) were evaluated based on genotyping of 29 genome-wide microsatellite loci. Fayoumi lines displayed the lowest within-population genetic diversity (MNA=4.24; HE=0.48-0.50) and least allelic privacy (PA=1(2%)) but showed its own distinct structure. Synthetic breeds displayed high genetic variation and uniqueness (MNA=4.59-5.31; HE=0.55-0.66; PA=3-9(2%-10%)), whereas unclear-admixed structure except for Gimmizah. This observation indicates sever integration of genetic entities of Fayoumi founders into synthetic breeds loosing the allelic barrier in between. AMOVA revealed greater genetic variation between the six strains (7%) than between three synthetic breeds (Gimmizah, Golden-Montazah and Bandara) (3%). Therefore, crossbreeding may dilute the aggregate diversity through intensive sharing gene pools of ancestral strains to create different synthetic hybrids. Mean values of Nei’s genetic-distances; 0.10, marker-estimated kinship (MEK); 0.13 and coancestry coefficient; 0.09 inferred considerable genetic differentiation, while, high genetic relatedness between strains studied. Nei’s genetic distance- and MEK-based phylogenies showed two major clusters: Fayoumi lines and Doki-4 (cluster 1) and other synthetic breeds (cluster2). Multivariate analysis and STRUCTURE demonstrated Fayoumi lines and Gimmizah as clearly separated populations, but other synthetic breeds as mosaic admixed populations. Regarding genetic variation and uniqueness, Gimmizah contributed the most to between-population and aggregate genetic diversity, Golden-Montazh contributed slightly higher to within-population genetic diversity, whereas Fayoumi lines added negatively to all components. Regarding genetic overlap, Fayoumi-GG and Doki-4 were the most overlapped with other strains; therefore, they were excluded from the core set in which Bandara was ranked firstly. In conclusion, Fayoumi lost its most genetic uniqueness due to intensive crossbreeding and introgression, thus it is in high need to be conserved. It is recommended molecular characterization of founder breeds utilized in crossbreeding and crossing between genetically distant and originally overlapped populations that could rescue the aggregate genetic diversity.