This study focused on the genotyping of Aeromonas hydrophila isolated from diseased Nile tilapia, virulence genes, and their relation with motile aeromonad septicemia (MAS) clinical signs, and the resistance profiles of the recovered isolates to the frequently used antimicrobials in aquaculture. We determined the prevalence of A. hydrophila and the associated mortality in fish in various farms. We also investigated the extent of homogeneity of isolates sampled from various aquaculture farms and fish organs and how these variables would drive A.hydrophila heterogeneity to help developing control strategies against this infection. Of the 41 (41%) A. hydrophila isolates recovered by culture from diseased fish in four aquaculture fish farms (faced 35–50% mortality rates) located at different geographical regions in Egypt, 39 (39%) were confirmed by 16S rDNA-PCR amplification. Five distinct patterns were found for the distribution of virulence genes among 41% of A. hydrophila isolates. Thirteen isolates (33.33%) were positive for aer gene; 9 (23.1%) harbored lip gene, 2 (5.13%) carried hlyA gene, and one isolate (2.56%) was positive for ast gene. A positive correlation was found between hlyA and ast, and between lip and aer genes (r =0.6 and 0.5, respectively). All isolates were resistant to ampicillin and amoxicillin. The least resistance was noted for doxycycline and gentamicin (7.7%) followed by streptomycin (10.3%), trimethoprim/sulfamethoxazole (17.9%), chloramphenicol (25.6%), colistin (43.6%), and erythromycin (47.7%). Most isolates were susceptible to ciprofloxacin. Multiple antimicrobial resistance index values ranged from 0⋅2–0⋅6 among multidrug-resistant (MDR) isolates (87⋅2%). Enterobacterial repetitive intergenic consensus (ERIC)-PCR allowed differentiating A. hydrophila isolates into 3 ERIC clusters, each contained isolates belonging to different farms and organs. The fingerprinting profiles of isolates were diverse without any obvious regional or organ-specific isolates. Our results indicated that sampling localities and sampled organs differ, albeit none substantially, in terms of the respective isolates heterogeneity. In conclusion, the high prevalence of A. hydrophila in Nile tilapia and its diverse antimicrobial resistance and virulence profile suggest the increased risk of this infection and raise concerns about its public health importance. The prudent use of antibiotics in the fish industry is now becoming mandatory to avoid the great losses in aquaculture due to MDR A. hydrophila. Our study also indicated the importance of ERIC genotyping for the analysis of A. hydrophila diversity during future molecular epidemiology investigations.