The relationship between Homo habilis and early African Homo erectus has been contentious because H. habilis was hypothesized to be an evolutionary stage between Australopithecus and H. erectus, more than a half-century ago. Recent work re-dating key African early Homo localities and the discovery of new fossils in East Africa and Georgia provide the opportunity for a productive re-evaluation of this topic. Here, we test the hypothesis that the cranial sample from East Africa and Georgia represents a single evolutionary lineage of Homo spanning the approximately 1.9–1.5 Mya time period, consisting of specimens attributed to H. habilis and H. erectus. To address issues of small sample sizes in each time period, and uneven representation of cranial data, we developed a novel nonparametric randomization technique based on the variance in an index of pairwise difference from a broad set of fossil comparisons. We fail to reject the hypothesis of a single lineage this period by identifying a strong, time-dependent pattern of variation throughout the sequence. These results suggest the need for a reappraisal of fossil evidence from other regions within this time period and highlight the critical nature of the Plio-Pleistocene boundary for understanding the early evolution of the genus Homo.