Estuaries are final depositional environments of sediments transported along rivers. Therefore, they give a generalized dimension about the human effluents released in water systems. The development of molecular techniques allowed the study of environmental DNA (eDNA), which can provide a real dimension about the functioning of the microbial communities of those environments and the impacts of human activities. In this context, antimicrobial resistance is an emerging problem, caused by irresponsible use of antimicrobial drugs in human and animal health, which has contributed to a selection of bacteria resistant to these drugs. The objective of this study is to identify the main phyla of bacteria and to detect the presence of Antibiotic Resistance Genes (ARGs) in different mangroves environments. We observed significant differences between ARGs quantity in each point. Samples collected on Guaibim-2 and Una had bigger diversity of ARGs, while Guaibim-1 had less AGRs diversity. The predominant phyla in all of the samples was Proteobacteria, Actinobacteria and Firmecutes. We detectedEnterococcus faecium, Acinetobacter sp, Klebsiella pneumoniae, Enterococcus faeciumandEnterobacter cloacae,listed bacteria for priority surveillance for World Health Organization on points Una and Guaibim-2.