Male and female Rock Shags (Phalacrocorax magellanicus) are not obviously sexually dimorphic in plumage or size and are thus difficult to distinguish in the field. We evaluated the utility of two different DNA-based techniques for sexing adult Rock Shags. We found that the primer set 2550F/2718R (originally tested in three individuals of P. carbo), with minor differences in the forward primer, provided a consistent and simple sexing method for Rock Shags. Moreover, we obtained three reliable discriminant functions for sexing adults from three different colony sites between 42° to 47°S in coastal Patagonia, Argentina. Discriminant analysis of five external characters of adult birds indicated that head, bill, and wing lengths were the most accurate variables for use in a discriminant function model, predicting the sex of 80–86% of the birds. Males were significantly larger than females for all body measurements except for bill depth. Rock Shags showed less marked sexual dimorphism than other phalacrocoraciid species.