The Magellanic penguin is the most commonly species of penguin found in temperate regions of South America. During the months of April to September, many of them are found stranded on coastal regions of Brazil, either dead or severely debilitated due to various adverse situations they face during their migratory period. Many of these debilities are due to infections caused by microorganisms present in the microbiota of these penguins, which take advantage of the immunosuppression of these birds to proliferate and generate clinical signs that can ultimately lead to their death. In the present study, several microbiological techniques were performed, including bacterial culture, antimicrobial susceptibility testing (antibiogram), fungal culture, and antifungal susceptibility testing (antifungigram) of samples that arrived from rehabilitation centers to the laboratory where the study was carried out. In the bacterial culture, the majority of the isolated bacteria belonged to the natural microbiota of the penguins, such as Klebsiella spp., Pseudomonas spp., and Escherichia coli. In the antibiogram, the antibiotics that showed the most resistance were cefalotin and amoxicillin, but what caught the attention in this test was the number of samples that presented multidrug resistance, being resistant to three or more classes of antimicrobials. Bacterial culture was also performed in a specific medium for the growth of Salmonella spp., but it did not yield positive results. Fungal cultures yielded growth of Aspergillus spp., whose antifungal susceptibility testing showed resistance to three antifungals and sensitivity to the other five antifungals tested. Further studies are necessary to understand the role of Magellanic penguins as sentinels in infections caused by environmental microorganisms. The observation of multidrug resistance to commonly used antibiotics highlights the importance of performing antimicrobial susceptibility testing for better therapeutic outcomes.