Objective This study was performed to compare the genetic diversity, virulence, and antimicrobial resistance of Aeromonas strains isolated from patients and healthy individuals. Methods A total of 38 clinical strains and 19 strains from healthy individuals were isolated from the samples collected in Ma'anshan City, Anhui Province. Their taxonomy was investigated using concatenated gyrB-cpn60 sequences, and their resistance to 12 antibiotics was evaluated. The pathogenicity of these strains was examined through beta-hemolysis, protease activity, and virulence gene assays. Results The 57 Aeromonas strains were divided into 55 sequence types. Of these types, 21 were novel, suggesting that their genetic diversity was high. These Aeromonas isolates could be divided into 7 species, and the positive rates of beta-hemolysis and protease activity were 49.1％ and 73.7％, respectively. The detection rate of clinical patients in terms of beta-hemolysis and protease activity was higher than that of healthy individuals. Among the four most common Aeromonas strains, A. dhakensis had the highest detection rate of virulence genes. The multidrug resistance rate of the clinical isolates was much higher than that of the strains isolated from healthy individuals. Conclusions The taxonomy, virulence properties, and antibiotic resistance of Aeromonas isolates from patients differ from those of the isolates from healthy individuals.