Vocal behavior can be an indicator of physiological state or genetic make-up, but has not been developed as a diagnostic tool in seabirds. Aptenodytes penguins lack external sexual dimorphism, but the sexes have dimorphic courtship calls. We present a case study in which unique call structure of an emperor penguin (Aptenodytes forsteri) was associated with a same-sex bonded pair. Typical males produce lower frequency calls with proportionally more long bursts, while typical females produce slightly higher frequency calls with proportionally more short bursts. We recorded two male emperor penguins (E-79 and E-81) at SeaWorld San Diego that behaved as a bonded pair. E-79 produced a call that was qualitatively different from the male type to human listeners. Using the Teager-Kaiser Energy Operator to visualize bursts, we calculated and compared burst rates of E-79 and E-81 to other emperor penguins in the SeaWorld colony and a colony at Cape Crozier, Antarctica. Analysis showed E-79’s calls had a unique burst rate structure that was intermediate between typical male and female patterns. Our results suggest that while emperor courtship calls are usually strongly sexually dimorphic, it is not always the case. The exceptions could provide interesting insights into call development, physiology, and/or genetics.