The Chloropidae is a species-rich family of flies with about 3000 species in four subfamilies. The Chloropinae is the second most species-rich subfamily with almost 1000 described species in 75 accepted genera. There is agreement about the monophyly of the subfamily; however, the relationships among the genera are still poorly understood and some genera are clearly paraphyletic. Thus, the interpretation of the evolution of morphological traits, such as male terminalia sclerites, remains challenging. This is the first phylogenetic study of the Chloropinae using a formal analytical approach, including representatives of 73 genera of the subfamily and 124 morphological characters. The monophyly of the Chloropinae is corroborated. Chloropella is sister to the remainder of the subfamily. Slightly different analytical procedures show stable clades and rogue taxa. We propose a system for the subfamily with ten tribes, three of which are newly proposed here—Chloropellini trib. nov., Chloropini, Chloropsinini trib. nov., Diplotoxini, Eurinini stat. nov., Lasiosinini, Mepachymerini, Meromyzini, Mindini and Pseudothaumatomyini. Eight genera are kept incertae sedis and two new genera are erected. There is compelling evidence that Chlorops and Ectecephalina are paraphyletic.