The illegal wildlife trade may increase the risk of infectious disease transmission, and it may not only cause disease outbreaks in humans but also threaten livestock, native wild populations, and ecosystems' health. Bird species may act as carriers in the transmission of enteric pathogens. However, epidemiological studies on zoonotic bacteria in wild birds are rare in Brazil. From March 2011 to March 2012, we investigated the frequency of Enterobacteriaceae in cloacal swab samples from 109 birds of the passerine and Psittacidae families. These birds were recovered from illegal trade in Rio de Janeiro, Brazil, and sent to a rehabilitation center. Gram-negative bacteria were isolated from 86 wild birds (78.9%). A mean (±SD) of 1.68 (±1.30) different bacterial species were isolated per bird, with a maximum of five bacterial species from three bird species. The most frequently isolated bacteria were Escherichia coli, followed by Enterobacter spp., Klebsiella pneumoniae and other enteric bacteria. Salmonella ser. Typhimurium was isolated from a Temminck's seedeater (Sporophila falcirostris), and two Salmonella ser. Panama were isolated from two specimens of chestnut-capped blackbird (Chrysomus ruficapillus). Of the 70 selected bacterial isolates, 60 exhibited antibiotic resistance. The resistance patterns varied from one to nine of the antibiotics tested. Resistance to ceftiofur was the most prevalent, followed by ampicillin and ceftriaxone. The dissemination potential of resistant strains in situations typically seen in the management of captive birds may become a problem for the conservation of natural bird populations and for public health.