Systematic relationships among Laniatores have received considerable attention during the past few years. Many significant taxonomic changes have been proposed, particularly in the superfamily Gonyleptoidea. As part of this superfamily, the basalmost Stygnopsidae is the least known family. In order to propose the first total evidence phylogeny of the family, we produced four datasets: three molecular markers – partial nuclear 28S, mitochondrial ribosomal 16S, mitochondrial protein-encoding cytochrome c oxidase subunit I; and 72 morphological characters. With these data, we performed three different phylogenetic analyses: (1) Bayesian Inference with molecular data, and (2) Bayesian Inference and (3) Maximum Likelihood using combined data. Our results are congruent: a monophyletic Stygnopsidae subdivided into two major clades: Stygnopsinae and Karosinae, subfam. nov. The following genera are redefined: Stygnopsis, Hoplobunus and Serrobunus stat. rev. The following taxa are described: Iztlina venefica, gen. nov., sp. nov. and Tonalteca, gen. nov. Additionally, the following changes are proposed: Serrobunus queretarius (Šilhavý, 1974), comb. nov., Stygnopsis apoalensis (Goodnight & Goodnight, 1973), comb. nov., Stygnopsis mexicana (Roewer, 1915), comb. nov., Stygnopsis oaxacensis (Goodnight & Goodnight, 1973), comb. nov., and Tonalteca spinooculorum (Goodnight & Goodnight, 1973), comb. nov. We also discuss the status of the genera Isaeus stat. rev. and Mexotroglinus. Finally, we discuss the evolution of male genitalia and convergence of selected homoplastic diagnostic characters.