A new species Aphaenogaster wennebergi Zharkov et Dubovikoff, sp. n. is described from late Eocene Danish amber. The holotype is the first known male of the genus Aphaenogaster Mayr from Late Eocene ambers and we consider it appropriate to describe it as a new species. Current classification problems of the ant genus Aphaenogaster and related taxa, both recent and fossil, are discussed. We also present a complete palaeoreconstruction of the new ant based on computer microtomography.