The structure of the male genitalia of three known cytotypes (A, B, and C) of Anopheles nuneztovari varies geographically. Morphometric analyses of 437 specimens revealed significant variation for collection sites within and among cytotypes. Most genitalic characters failed to distinguish cytotypes. Four characters distinguish cytotype B males of the other two cytotypes. The aedeagal leaflets are longer and more heavily sclerotized, the parabasal tubercle is shorter, and the larger accessory seta is shorter among cytotype B males. Specimens lacking leaflets on both sides of the aedeagus were observed only among cytotype A. Within cytotype A progeny broods, 6.7-21% of specimens lacked both leaflets. Considerable overlap of characters exists between the male genitalia of cytotypes A and C. The results of morphological analyses are contrasted with findings from recent molecular studies. Characters of the male genitalia appear to be of limited utility for delimiting the probable relationships among cytotypes of Anopheles nuneztovari sensu lato.