The aim of the present study was to evaluate the effect of polymorphisms in the ATP-binding cassette subfamily G member 2 (ABCG2), growth hormone (GH) and growth hormone receptor (GHR) genes on 305-day yields and milk traits in native Egyptian cattle (Baladi), Holstein Friesian cattle and hybrid cattle using DNA sequencing and Restriction Fragment Length Polymorphisms (RFLPs). A total of 148 cows were selected from the three animal populations. The ABCG2-HhaI-AA genotype was significantly associated with an increased milk lactose percentage and reduced milk yields in Baladi cows. The GH-MSP1-heterozygous genotype (GH) showed significant associations with SNF, protein and lactose percentages in the hybrid cows. Fewer TG repeats were found in the 5' untranslated region of GHR in Baladi cows, which could be used for marker-assisted selection to protect against the lower milk yields observed in this population. Additionally, GHR-MSP1-VL, can be associated with higher SNF, fat, protein and lactose percentages in hybrid cows, as well as lower milk yields in Baladi cows. We concluded that the three cattle populations have their own genetic identities in relation to genetic markers, which can be used for marker-assisted selection to improve milk traits in these three cattle populations.