Mosquitoes of the genus Haemagogus are important vectors of yellow fever virus and other arboviruses and are the principal reservoirs of these viruses in nature. Haemagogus capricornii and Haemagogus janthinomys are closely related species between which females are morphologically cryptic. A morphometric study of these species was performed on male and female specimens from 14 municipalities in Brazil. Morphometric analyses were able to distinguish females. Multivariate morphometrics may be a useful tool for taxonomic studies of cryptic species in this group.