In this study, we present the first attempt at a molecular phylogenetic analysis of the entire family of Cordulegastridae involving 60% of its known species. Our analysis is in favor of reclassification of the members of the family into four genera: (i) the monophyletic genus Anotogaster Selys, 1854, with the number of known species reduced by three synonymizations; (ii) the genus Cordulegaster Leach in Brewster, 1815 including all members of the boltonii group and, as a preliminary solution, the American species C. virginiae Novelo-Gutiérrez, 2018 and, very tentatively, C. diadema Selys, 1868. The bidentata group forms a genus of its own, for which we restored the name Thecagaster Selys 1854, stat. rev. Cordulegaster pekinensis McLachlan in Selys, 1886, currently considered as Neallogaster pekinensis, was placed by us in Thecagaster as well. The genus Neallogaster Cowley, 1934 needs further investigation involving all remaining species listed in it. The genus Zoraena Kirby, 1890, stat. rev., was recovered to accommodate the remaining American species of Cordulegaster. We synonymized three species of Anotogaster: Anotogaster gregoryi Fraser, 1923 = Anotogaster xanthoptera Lohmann, 1993, syn. nov.; Anotogasterkuchenbeiseri (Förster, 1899) = Anotogaster antehumeralis Lohmann, 1993, syn. nov.; Anotogaster kuchenbeiseri (Förster, 1899) = Anotogaster cornutifrons Lohmann, 1993, syn. nov., based on examination of the existing type specimens. The type of specimens of A. klossi Fraser, 1919 = A. flaveola Lohmann 1993 syn. confirm., were also examined, and their synonymy was confirmed. The isolated populations of A. sieboldii (Selys, 1854) from the archipelagos of Okinawa and Amami Oshima in Japan, respectively, should be regarded as separate species, which will be described elsewhere. Furthermore, we suggest the synonymization of Cordulegaster parvistigma Selys 1873 syn. nov. with Thecagaster brevistigma (Selys 1854) comb. restaur.