The aims of this study were to characterize the choanal and cloacal aerobic bacterial flora in healthy captive green iguanas and to compare it with the bacterial flora of the biofilm present in the water container of each terrarium. Samples were collected from the choana and the cloaca of 20 healthy captive adult green iguanas and from the biofilm of 15 water containers. The final identification of aerobic bacteria was performed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.Salmonellapositive samples were serotyped. The most common strains observed at each test location were from 1) choanae:Staphylococcusspp.,Enterobacter cloacaeandComamonas testosteroni; 2) cloacae:Citrobacterspp.,Salmonellaspp. andCorynebacteriumspp.; and 3) biofilms:Pseudomonasspp.,Salmonellaspp. andAcidovoraxspp. We showed that apart fromSalmonellaspp., the choanal and cloacal bacterial flora differed from the microorganisms present in the biofilm of the animal’s water container. These data revealed that healthy captive adult green iguanas harbored several aerobic bacterial strains that in immunosuppressed reptiles may act as opportunistic pathogens. Also, several of the aerobic bacteria identified in samples are potential zoonotic agents. Characterization of the normal background flora in captive reptiles and their environment can contribute to an understanding of the spread of bacterial contamination and the risk of potential zoonotic diseases for people in contact with these animals.