Aeromonas hydrophilais a ubiquitous fish pathogen and an opportunistic human pathogen. It is mostly found in aquatic habitats, but it has also been isolated from food and bottled mineral waters. It causes hemorrhagic septicemia, ulcerative disease, and motileAeromonassepticemia (MAS) in fish and other aquatic animals. Moreover, it might cause gastroenteritis, wound infections, and septicemia in humans. Different variables influenceA. hydrophilavirulence, including the virulence genes expressed, host susceptibility, and environmental stresses. The identification of virulence factors for a bacterial pathogen will help in the development of preventive and control measures. 95Aeromonasspp. genomes were examined in the current study, and 53 strains were determined to be validA. hydrophila. These genomes were examined for pan- and core-genomes using a comparative genomics technique.A. hydrophilahas an open pan-genome with 18,306 total genes and 1620 genes in its core-genome. In the pan-genome, 312 virulence genes have been detected. The effector delivery system category had the largest number of virulence genes (87), followed by immunological modulation and motility genes (69 and 46, respectively). This provides new insight into the pathogenicity ofA. hydrophila. In the pan-genome, a few distinctive single-nucleotide polymorphisms (SNPs) have been identified in four genes, namely:d-glycero-beta-d-manno-heptose-1,7-bisphosphate 7-phosphatase, chemoreceptor glutamine deamidase, Spermidine N (1)-acetyltransferase, and maleylpyruvate isomerase, which are present in allA. hydrophilagenomes, which make them molecular marker candidates for precise identification ofA. hydrophila. Therefore, for precise diagnostic and discrimination results, we suggest these genes be considered when designing primers and probes for sequencing, multiplex-PCR, or real-time PCR.