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Ancient DNA from the Mediterranean has revealed long-range connections and population transformations associated with the spread of food producing economies. But in contrast to abundant data from Europe, data from this key transition in northern Africa have only been available from the far western Maghreb (Morocco). We present whole genome data for nine individuals from the Later Stone Age (LSA) through the Neolithic in Algeria and Tunisia. The earliest cluster with pre-Neolithic people of the western Maghreb ( 15000–7600 BP), showing that this “Maghrebi” ancestry profile had a substantial geographic and temporal extent. At least one individual from Djebba (Tunisia), dating to 8000 BP, harbored ancestry from European hunter-gatherers, likely reflecting early Holocene movement across the Strait of Sicily. Later Neolithic people from the eastern Maghreb retained largely local forager ancestry as well as smaller contributions from European farmers (by 7000 BP) and Levantine groups (by 6800 BP), and were thus far less impacted by external gene flow than other parts of the Neolithic Mediterranean.