Stratiomyidae is a diverse, cosmopolitan family of Diptera (true flies). One of its twelve subfamilies, Clitellariinae, is distributed in all major biogeographic regions except Antarctica. Understanding the evolutionary history of Clitellariinae is key to reconstructing the phylogeny of Stratiomyidae as a whole because Clitellariinae is united only by shared ancestral characters. The current research investigates the relationships between the genera currently placed within the Clitellariinae, and the relationships of all the subfamilies of Stratiomyidae using morphological and molecular techniques. Morphology was analyzed with the method of parsimony at the generic level using 100 adult characters. Molecular analyses were performed with parsimony and Bayesian methods, using the Elongation Factor one alpha and 28S ribosomal genes. Morphological and molecular trees were not wholly congruent with respect to placement of clitellariine genera, but indicated that Clitellariinae are not monophyletic. Trees were congruent with respect to monophyly of all other subfamily clades within Stratiomyidae, with the exception of Stratiomyinae. Both morphology and gene sequences supported the groupings of (Dicyphoma + Cyphomyia), and (Abavus + Acropeltates), as well as subfamilial relationships of (Sarginae + Hermetiinae) and (Stratiomyinae + Raphiocerinae). Combined morphological and molecular analyses, aspects of character evolution, and biogeographical distribution were also explored.