Insect genitalia are complex, subject to sexual selection and homoplasy, and difficult to interpret phylogenetically. They can provide useful phylogenetic signal, however, given an understanding of homology. In hydropsychid caddisflies (Insecta: Trichoptera), and particularly in the subfamily Hydropsychinae, the evolutionary patterns and homologies of the male genitalia have been the source of long-standing debate. Using confocal microscopy and 3-D image reconstruction, we focused in detail on three structures of the hydropsychid phallic apparatus: 1) phallotremal sclerites, 2) endotheca, and 3) endophallus. We then used Mesquite© software (Version 1.11) to map these characters onto a phylogeny of Hydropsychidae that was independently constructed using nuclear ribosomal and mitochondrial COI sequences as well as morphology (excluding genitalia). This technique revealed patterns among subfamilies and genera in the presence, modification, and internal arrangements of these phallic structures. These patterns were obscured previously by limited taxonomic scope and homoplasy (specifically symplesiomorphies and convergences). Our study suggests that while the endophallus appears to be a synapomorphy for the Hydropsychinae, the endotheca may have evolved or been modified multiple times within Hydropsychidae. Several questions remain on the origin and homology relationships of the "phallotremal" sclerites.