Knowledge of the male genitalia of the Atemnidae is still limited, although several authors have previously contributed to our understanding of their structure. This study deals with the morphology and configuration of the male genital organs. Forty-four species belonging to 16 different genera have been investigated, including species of 4 genera of Miratemninae. Anatemnus longus Beier 1932 is synonymized with A. voeltzkowi (Ellingsen 1908), Paratemnoides ceylonicus (Beier 1932) is synonymized with P. pallidus (Balzan 1892), and P. minor (Balzan 1892) with P. nidificator (Balzan 1888). Tamenus equestroides (Ellingsen 1906) is moved to the genus Cyclatemnus. The genitalia of the investigated specimens are described and a general diagnostic description of the male genitalia of the family is given. The study reveals an overall uniformity in the genitalic configuration of the family, which indicates monophyly. With respect to the affinities with other families of the Cheliferoidea, the male genitalia suggest that the Atemnidae might be closer to the Withiidae than to the Cheliferidae or Chernetidae. Claimed differences between the Atemninae and Miratemninae are considered, but the morphology of the male genitalia does not support their division into two families. Comparison of species of the genera Anatemnus, Catatemnus, Oratemnus and Paratemnoides reveals greater variation within the genera than between different genera. This infers that the present systematic grouping of species does not reflect true phylogenetic relationships within the family.