Management strategies associated with captive breeding of endangered species can establish opportunities for transfer of pathogens and genetic elements between human and animal microbiomes. The class 1 integron is a mobile genetic element associated with clinical antibiotic resistance in gram-negative bacteria. We examined the gut microbiota of endangered brush-tail rock wallabies Petrogale penicillata to determine if they carried class 1 integrons. No integrons were detected in 65 animals from five wild populations. In contrast, class 1 integrons were detected in 48% of fecal samples from captive wallabies. The integrons contained diverse cassette arrays that encoded resistance to streptomycin, spectinomycin, and trimethoprim. Evidence suggested that captive wallabies had acquired typical class 1 integrons on a number of independent occasions, and had done so in the absence of strong selection afforded by antibiotic therapy. Sufficient numbers of bacteria containing diverse class 1 integrons must have been present in the general environment occupied by the wallabies to account for this acquisition. The captive wallabies have now been released, in an attempt to bolster wild populations of the species. Consequently, they can potentially spread resistance integrons into wild wallabies and into new environments. This finding highlights the potential for genes and pathogens from human sources to be acquired during captive breeding and to be unwittingly spread to other populations.