In this study, we describe the previously unknown male of the spider Clitaetra thisbe Simon, 1903, from Sri Lanka and provide some data on its natural history. In light of this new information, we present results from the first cladistic analyses of Clitaetra species that include male morphological characters of C. thisbe and DNA sequence data for representatives of all nephilid genera and a broad sample of outgroups. The monophyly of Clitaetra and the basal position of C. thisbe within the genus are corroborated. Our results also support the hypothesis that Nephila is a sister group to the clade Herennia Nephilengys, which challenges the current hypothesis for nephilid relationships that has been used extensively for the study of genitalic and web evolution in Nephilidae. We also discuss some of the previously proposed interpretations and primary homology statements for several male genitalic characters in nephilids.