Respiratory infections are common in young wombats and determining the causative agent is critical to establish an appropriate treatment. A group of 12 young, wild common wombats (Vombatus ursinus) ranging from 6 to 10 kg developed a range of respiratory signs after being in care following the severe bushfires in Australia in early 2020. The oral anatomy of wombats makes collection of tracheal samples difficult. An endoscopy-guided technique was established to collect microbiology samples aseptically from the anesthetized patients. A guarded, sterile swab was introduced in the mouth and inserted into the trachea of two wombats, visualizing the procedure with the endoscope. A similar technique is described for endotracheal intubation of small mammals. This approach allowed for a safe and aseptic sampling collection. A pure growth of Escherichia coli was cultured from the samples, and appropriate antibiotic treatment was established according to the antimicrobial sensitivity test.