Degrees and patterns of morphological sexual dimorphism are problematic characters for the purpose of phylogenetic analysis. Since sexual dimorphism is a product of at least partly independent selection in males and females – although the underlying genetics of certain characters can produce a correlated response (Plavcan, 1998) – the relative contributions of male and female values to any measure of sexual dimorphism will vary. For example, species of Hylobates and Callicebus both have very minimal canine size dimorphism (Plavcan & van Schaik, 1992), but in Hylobates this is achieved through female canine hypertrophy, whereas in Callicebus it results from male canine reduction (Plavcan et al., 1995). Therefore, similar or identical measures of sexual dimorphism will not necessarily be homologous and can instead reflect homoplasy. Moreover, even sexual dimorphisms that reflect similar contributions from male and female values in the different species can still result from homoplasy; species of Hylobates and the Pitheciinae all express low levels of canine size dimorphism as a result of female canine hypertrophy, but this has clearly evolved independently in the two lineages. While the possibility of homoplasy exists for any character, it has quite clearly been especially common with respect to sexual size dimorphism, including canine size dimorphism, both within and between higher primate lineages.

While sexual dimorphisms as a class of characters offer poor prospects for phylogenetic reconstruction, it is nevertheless legitimate to explore the phylogenetic significance of morphological characters that happen to be sexually dimorphic. However, this can only be done in males and females separately since, by definition, males and females express different states for sexually dimorphic characters.