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Simple Summary: The production of domestic geese in Egypt depends mainly on small-sized flocks reared by smallholder farmers in villages, and until now, there have been no intensive or commercial goose farms in Egypt. The objective of this study was to characterize three domestic Egyptian goose populations (Kafr El-Sheikh, Fayoum and Luxor) phenotypically and genetically in order to identify the populations with the highest diversity to establish a large base population with a broad variation. Phenotypic characterization of 402 domestic mature geese included morphological measurements such as head length, culmen length, bill width, tarsus length, sternum length and chest circumference. Genetic characterization of 173 individuals was performed based on mutations in the mitochondrial D-loop region and the genotyping of 12 microsatellite markers. The results showed low population differentiation based on morphological measurements and low genetic differentiation based on the two used genetic markers. The low differentiation between the three investigated goose populations implies their suitability for aggregation and formation of a large founder population with high genetic variation. The information from this study could be useful for further investigation in order to develop a convenient conservation program for this important species. The objectives of this study were to achieve phenotypic characterization of three domestic Egyptian goose populations collected from three different geographical zones (Kafr El-Sheikh, Fayoum and Luxor) and to perform genetic characterization of these three populations based on mtDNA D-loop and 12 microsatellite markers. The body measurements of 402 domestic mature geese belonging to these three governorates showed that the lengths of the head, culmen and tarsus and the live body weight varied significantly among the three studied Egyptian goose populations. After alignment of a 710-base-pair segment of the goose mtDNA control region, there was a single haplotype in the three Egyptian goose populations, indicating the same maternal origins. The genotyping of the 12 microsatellite markers showed low diversity indices, including average observed (NA) and effective (NE) number of alleles and observed (HO) and expected heterozygosity (HE) (3.333, 1.760, 0.277 and 0.352, respectively), and a high inbreeding coefficient (FIS = 0.203) across the three Egyptian goose populations. The high inbreeding and low genetic and morphological differentiation of Egyptian geese could be corrected by establishing a large base population through capturing small populations with the highest genetic variation. The findings of the current study can therefore serve as an initial guide to design further investigations for developing conservation programs of Egyptian geese genetic resources. [ABSTRACT FROM AUTHOR]