This study aimed to isolate and identify Aeromonas bacteria from samples of oysters and water, by microbiological and molecular methods. Identification of Aeromonas was performed by the conventional method and by PCR and species characterization was performed by identification key Aerokey II and by RFLP-PCR of 16S rDNA. 59 (98.3%) samples of oysters and 15 (75%) samples of water contaminated by Aeromonas bacteria were identified. Of the 74 isolates of Aeromonas spp. obtained by microbiological analysis, 53 (71.62%), 38 (65.51%) oyster samples and 15 (100%) of water samples confirmed the characterization of the genus by molecular technique. As to biochemical species identification, 59.3% (n = 35) and 40.6% (n = 24) of isolates from Aeromonas sp. obtained from oyster samples were rated as A. hydrophila and A. caviae, respectively; and from isolates obtained from water samples, 60% (n = 9) were classified as A. hydrophila and 40% (n = 6) as A. caviae; however, only the A. hydrophila was confirmed by genetic sequencing. Regarding the classification by RFLP-PCR 16S rDNA, patterns of nonspecific bands were obtained, making it impossible to identify the species by this technique. The large number of oyester samples contaminated with Aeromonas spp. and identification of A. hydrophila, demonstrate that this mollusk might present a risk to consumer health, mainly because it is consumed raw and is to a potentially pathogenic micro-organism to humans.