Sexual call dimorphism in birds is usually associated with sexual size dimorphism. Departures from this relationship can be used to infer call function, but research into inter-sexual call differences, as with song function in general, has been restricted by a bias towards male passerines. The nocturnal and flightless New Zealand kiwi (Apterygidae) are acoustically similar but taxonomically and ecologically very different from other birds, so provide a contrast in exploring avian call function and evolution. However, kiwi acoustic ecology is poorly understood, with the calls of only one of the five kiwi species spectrally described, and acoustic differences between the sexes virtually unknown. We conducted the first bioacoustic study of Little Spotted Kiwi Apteryx owenii, and assessed sexual call dimorphism in this species. There were significant inter-sexual differences in call temporal and frequency characteristics that were not related to size dimorphism. Contribution to duets and variation in temporal structure with call context also differed between the sexes. We suggest that these differences indicate divergent call function, with male calls more suited for territory defence, and female calls for pair contact. There was a striking lack of overlap in the frequency spectrum distributions of male and female calls, which was also unrelated to size and was further emphasized by the presence of formants in female calls. We propose that this provides evidence for inter-sexual acoustic cooperation in call frequency, of a type which to our knowledge has not previously been described in birds. This may result from selection for enhanced joint resource defence in kiwi.