Initially, Nanantius eos was classified as an enanthiornithine, a Cretaceous group of primitive birds that did not survive the Cretaceous–Paleogene mass extinction. However, it is now known that the characters of the tibiotarsus are not sufficiently diagnostic to place a bird into the Enantiornithes. For example, the more modern genus Apsaravis also possessed an "enantiornithine" tibiotarsus (Clarke & Norell, 2002). Thus, although an enantiornithine affinity of Nanantius is likely - these birds were the dominant avian group in the Early Cretaceous, and the tibiotarsus is very similar to the doubtlessly enantiornithine Gobipteryx -, this placement is not certain until more diagnostic material, such as the characteristic tarsometatarsi, have been found.