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Aquaculture is a growing sector, providing several products for human consumption, and it is therefore important to guarantee its quality and safety. This study aimed to contribute to the knowledge of bacterial composition of <i>Crassostrea gigas</i>, <i>Mytilus</i> spp. and <i>Ruditapes decussatus</i>, and the antibiotic resistances/resistance genes present in aquaculture environments. Two hundred and twenty-two bacterial strains were recovered from all bivalve mollusks samples belonging to the <i>Aeromonadaceae</i>, <i>Bacillaceae</i>, <i>Comamonadaceae</i>, <i>Enterobacteriaceae</i>, <i>Enterococcaceae</i>, <i>Micrococcaceae</i>, <i>Moraxellaceae</i>, <i>Morganellaceae</i>, <i>Pseudomonadaceae</i>, <i>Shewanellaceae</i>, <i>Staphylococcaceae</i>, <i>Streptococcaceae</i>, <i>Vibrionaceae</i>, and <i>Yersiniaceae</i> families. Decreased susceptibility to oxytetracycline prevails in all bivalve species, aquaculture farms and seasons. Decreased susceptibilities to amoxicillin, amoxicillin/clavulanic acid, cefotaxime, cefoxitin, ceftazidime, chloramphenicol, florfenicol, colistin, ciprofloxacin, flumequine, nalidixic acid and trimethoprim/sulfamethoxazole were also found. This study detected six <i>qnrA</i> genes among <i>Shewanella algae</i>, ten <i>qnrB</i> genes among <i>Citrobacter</i> spp. and <i>Escherichia coli</i>, three <i>oqxAB</i> genes from <i>Raoultella ornithinolytica</i> and <i>bla</i>_TEM-1 in eight <i>E. coli</i> strains harboring a <i>qnrB19</i> gene. Our results suggest that the bacteria and antibiotic resistances/resistance genes present in bivalve mollusks depend on several factors, such as host species and respective life stage, bacterial family, farm’s location and season, and that is important to study each aquaculture farm individually to implement the most suitable measures to prevent outbreaks.