This study addresses the relationship between cranial metric variables and nonmetric traits using the skeletal sample of rhesus macaques from Cayo Santiago. Discriminant function analysis is used to study the metric differences between macaque crania grouped according to the presence or absence of nine nonmetric traits. The computation of total structure coefficients from the discriminant function analyses provides information regarding how closely each metric variable is related to the discriminant functions derived. Total structure coefficients have not been used previously in the study of the relationship between metric and nonmetric traits. The results of the analysis are interpreted using an explicit approach to cranial morphogenesis—functional cranial analysis. It is concluded that the relationship between cranial metric and nonmetric traits is explicable in terms of a common developmental pathway shared by the two types of traits. Identification of the specific etiology of nonmetric traits depends on future anatomical studies of organisms throughout the period of nonmetric trait development.