Several hypotheses posit a link between the origin of Homo and climatic and environmental shifts between 3 and 2.5 Ma. Here we report on new results that shed light on the interplay between tectonics, basin migration and faunal change on the one hand and the fate of Australopithecus afarensis and the evolution of Homo on the other. Fieldwork at the new Mille-Logya site in the Afar, Ethiopia, dated to between 2.914 and 2.443 Ma, provides geological evidence for the northeast migration of the Hadar Basin, extending the record of this lacustrine basin to Mille-Logya. We have identified three new fossiliferous units, suggesting in situ faunal change within this interval. While the fauna in the older unit is comparable to that at Hadar and Dikika, the younger units contain species that indicate more open conditions along with remains of Homo. This suggests that Homo either emerged from Australopithecus during this interval or dispersed into the region as part of a fauna adapted to more open habitats.