Sex identification of adult cetaceans is an important ecological parameter that should be incorporated into studies such as population dynamics and animal behavior. In Cuvier's beaked whale (Ziphius cavirostris), sex determination may be achieved through genetics, observation of genitals, the presence/absence of erupted teeth, and calf association. However, these features are difficult to ascertain due to the shy behavior of this species. Therefore, this study aimed to create a robust sex identification method using only external characteristics. Particularly, this work analyzed pigmentation patterns and levels of natural marks from adult individuals of known sex in order to identify gender differences, using frequency analysis and generalized linear models. Photographic captures of 73 free-ranging animals were utilized. The frequencies of the individual pigmentation patterns were found to be sex dependent. The 63% of the animals could be classified into either a “soft” or “sharp” pigmentation cluster. The “soft” cluster was only displayed by females, while the “sharp” cluster was present in both the sexes. However, the model selection process indicated that natural marking is the best determinative factor for sex classification. The density of the visible intraspecific natural marks was found to differ between the sexes (P value < 0.001) and was incorporated as a predictor variable into several candidate models. All candidate models had a high predictive power (mean area under the curve 0.973) and correctly predicted the sex, by means of a density threshold value, in 85–90% of the analyzed animals. The density threshold ranged from 4.1% to 6.4% according to the different body area analyzed. These density threshold values represent a robust post hoc sexing method to classify individuals to sex from opportunistic photos in the absence of other sexing methods.