A 4-yr-old male captive hooded seal (Cystophora cristata), previously diagnosed as hypothyroid, died after a 3-wk period of lethargy and inappetance despite treatment that included intramuscular administration of antibiotics and multivitamins. Gross pathologic findings included extensive muscle necrosis over the left flank, an underlying necrotic iliac lymph node, two necrotic pulmonary masses and a necrotic bronchial lymph node. Routine cultures yielded a number of bacterial isolates and a heavy pure fungal growth from the necrotic iliac lymph node; wet preparations of which revealed sporangiophores typical of Mucor sp. Histopathology of necrotic muscle, pulmonary lesions and bronchial and iliac lymph nodes revealed necrosis with a marked pyogranulomatous and eosinophilic inflammatory cell infiltrate and fungal hyphae consistent with a Zygomycete species. This is believed to be the first report of systemic mucormycosis in a pinniped likely to have originated from an injection site reaction.