The Yellow-eyed Penguin (Megadyptes antipodes) is monomorphic but exhibits subtle sexual morphometric dimorphism. Information on the sexes of these birds is needed for informed management of the species and the construction of accurate population models. Using DNA analysis and Discriminant Function Analysis on head and foot measurements, we tested whether adults and fledglings of Yellow-eyed Penguin can be sexed using morphometry. We found that head and foot measurements can be used to correctly sex up to 93% of adults. Using only foot length, 88% of fledglings can be sexed accurately. As age until fledging was found to have an effect on morphometric variables, sexing should be conducted as synchronized as possible when chicks are over 90 days of age. We recommend that error rates inherent in sexing fledglings be taken into account when publishing sex-ratio data and subsequent analyses, particularly when age of fledglings could not be determined. The use of whole-skull measurements for sexing may be useful in other species in which bill measurements between the sexes are only slightly dimorphic or contains large degrees of overlap.