The purpose of this study was to describe the clonal diversity of Staphylococcus aureus strains derived from healthy dairy cattle and buffaloes as well as their close contact caretakers from the Nile Delta region, Egypt during 2019 and 2020, and to determine their antimicrobial resistance genotypes and virulence determinants. The study included 360 samples (120 from each, dairy cattle, buffaloes and their contact caretakers) collected from eight smallholding dairy herds.The samples included udder skin swabs, composite milk samples and rectal swabs (40 samples each of bovines) and nasal swabs, hand swabs and stool specimens (40 samples each of caretakers). S. aureus were isolated by classical techniques and characterised using the DNA microarray technology. A total of 62 methicillin-resistant (MRSA) and 130 methicillin-sensitive (MSSA) S. aureus isolates were identified. MRSA carriage rate ranged between 2.5% - 15% (Mean: 10%) in dairy cattle, 5% - 15% (9.2%) in dairy buffaloes and 27.5% - 37.5% (30.8%) among the caretakers. Nine different clonal lineages of MRSA (including CC22, CC152, CC5, CC30, CC88, CC45, CC121, CC97, and CC15), and six clonal lineages of MSSA (CC97, CC50, CC188, CC361, CC15 and CC1278) were inferred. The study demonstrated, for the first time, a high clonal diversity of multi-drug resistant S. aureus clones (particularly CC152-MRSA-V, CC30-MRSA-IV, CC121- MRSA-V, CC15-MRSA-V, CC97-MRSA-PseudoSCCmec, CC361-MSSA and CC1278-MSSA) which colonise dairy cattle and buffaloes as well as their caretakers particularly in Damietta villages that located at the northern Mediterranean coast of Egypt. The findings highlight the potential dynamics of humans and animals’ S. aureus strains which may represent a health threat for both populations. The complete absence of the lukM/lukF-P83 genes in the recovered isolates indicated that all recovered cattle isolates (except for CC97) were descendants of human lineages and that these replaced the original cow lineages. Hence, a recommendation was given to farm owners to review their hygiene regimen to help minimize the microbiological risks for both populations.