Here we present genomic data from 5 individuals dating to ca. 3000-2800 BCE from the Dzungarian Basin and 13 individuals dating to ca. 2100-1700 BCE from the Tarim Basin, representing the earliest yet discovered human remains from north and south Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, while the Early-Middle Bronze Age Tarim individuals only harbor a local ancestry. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian speaking pastoralists descended from the Afanasievo or to have originated among the BMAC or IAMC cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighboring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.