 This species is known from over 100 specimens collected from the earliest Ypresian Ølst and Fur Formations, found in calcareous rocks. The specimens were first studied and described by Jes Rust and N. Møller Andersen in 1999, and they named the species for Rebekka Madsen who collected the type specimen in September 1994. The holotype and paratype queen described are well preserved, although the legs are missing; the part and counterpart, GMUC No. 1995 8B and GMUC No. 1995 8A are deposited in the Geological Museum of the University of Copenhagen. At that time, Rust and Andersen placed the species into the modern ponerin genus Pachycondyla based on the shape of the abdominal segment VI and lack of dentition on the mandibles. Archibald, Cover, and Moreau moved the species to Ypresiomyrma based on the similarity to the McAbee species, by the shape of the abdominal segment III, which differs from that found in the Ponerinae subfamily genera, and by the morphology of the petiole. Y. rebekkae can be distinguished from other species by the shape of its petiole and the size of its head, being notably larger than Y. bartletti. The ants' somewhat angular head is also different, with other species having a rounded head. The species is known almost exclusively from queens, with only one known male ant assigned to it by Rust and Andersen.
