Female genital morphology of secondarily haplogyne spiders has been poorly studied, hampering the analysis of its possible phylogenetic significance. We conduct a comparative morphological study of 12 species of the secondarily haplogyne spider genus Glenognatha Simon, 1887 using scanning electron microscopy. Representatives of the closely related genera Pachygnatha Sundevall, 1823 and Dyschiriognatha Simon, 1893 were also examined. The female genitalia of Glenognatha, Dyschiriognatha, and Pachygnatha species examined are composed of a spiracle-shape gonopore, a membranous chamber, a pair of copulatory ducts (CD) leading to spermathecae and a large uterus externus (UE). The most significant variation among Glenognatha species, previously unregistered within Araneoidea, is related with the absence or presence of CD and spermathecae. In addition, several characters as the form and distribution of long stem gland ductules and compartmentalization of the UE may be important for phylogenetic inference at species and generic level. Our results corroborate the close relationship between Dyshiriognatha and Glenognatha. A table with potentially informative female genitalic characters for phylogenetic inference within Glenognatha is provided. Understanding the general structure of the female genitalia in secondarily haplogyne taxa is a crucial step in order to propose characters for phylogenetic inference and to understand its possible functional significance. J. Morphol. 275:1027–1040, 2014. © 2014 Wiley Periodicals, Inc.