Caatinga is a biome unique to Brazil, where degradation caused by anthropogenic actions has led to loss of biodiversity and put many species at risk of extinction. The Ceará state is located within the Caatinga and has a rich avifauna. It comprises 433 species, including 13 species that are in danger of extinction, which are found in the Baturité Massif. The aim of this study was to investigate the frequency and diversity of enterobacteria in wild birds and determine their susceptibility to antimicrobials. Cloacal swab samples were collected from 50 individuals of 28 different species, including the Ceara Gnatheter (Conopophaga cearae) and the Red-necked Tanager (Tangara cyanocephala), which are classified as vulnerable (VU) by the Brazilian Ministry of the Environment. A total of 55 isolates belonging to 14 different species of Enterobacteriaceae were identified. Among them, Pantoea agglomerans and Escherichia coli were the most prevalent species with isolation rates of 36% and 26%, respectively. The highest rate of antimicrobial resistance found was to ampicillin (41.8%), followed by nalidixic acid (36.3%) and amoxicillin associated with clavulanic acid (32.7%). Drugs that presented best efficacy were tobramycin (96.4%), ciprofloxacin (92.6%), and tetracycline (90.9%). Multidrug resistance was observed in 23.5% of the analyzed strains. This research provides important information about the composition of the cloacal microbiota of wild birds in Mulungu, Brazil, as well as their health status. Additionally, these results demonstrate that they harbor multidrug-resistant strains of Enterobacteriaceae.