Over a 25-mo span from a single zoologic collection, two bufflehead ducklings (Bucephala albeola) presented with pelvic limb paresis and were euthanized. On postmortem examination, the first duckling had intralesional fungal hyphae consistent with Aspergillus sp. in the spinal vertebrae and within pulmonary granulomas. In the second duckling, evidence of a thoracic spinal lesion was detected antemortem by using thermographic imaging. At postmortem examination, fungal hyphae consistent with Mucor sp. were found within the vertebrae. Although fungal infections of the respiratory system are commonly reported in waterfowl, infections that involve the spinal cord and vertebrae are unusual. These cases highlight the importance of consideration of axial skeleton fungal disease in neurologic presentations and the use of thermography for noninvasive diagnostic screening.