We have previously described hominin remains with numerous archaic traits from two localities (Maludong and Longlin Cave) in Southwest China dating to the Pleistocene-Holocene transition. If correct, this finding has important implications for understanding the late phases of human evolution. Alternative interpretations have suggested these fossils instead fit within the normal range of variation for early modern humans in East Asia. Here we test this proposition, consider the role of size-shape scaling, and more broadly assess the affinities of the Longlin 1 (LL1) cranium by comparing it to modern human and archaic hominin crania. The shape of LL1 is found to be highly unusual, but on balance shows strongest affinities to early modern humans, lacking obvious similarities to early East Asians specifically. We conclude that a scenario of hybridization with archaic hominins best explains the highly unusual morphology of LL1, possibly even occurring as late as the early Holocene.