From 7000 bc onwards, human groups are again present in the Nile Valley, but the number of Epipalaeolithic sites is very limited, and they have only been discovered in exceptional circumstances. Thus, only two cultures—the Elkabian and the Qamnian—can be distinguished. During the Epipalaeolithic, there was a continuation of the Palaeolithic style of subsistence, based on hunting, fishing, and gathering.
At Elkab, a few small Epipalaeolithic sites, dating to about 70006700 BC, have been found in an exceptionally good state of preservation because they are located within the far more recent Dynastic-Period enclosure wall. The sites were located on the beach of a silting-up Nile branch, the occupations having taken place after the floodplain inundations. The Epipalaeolithic fishing practices were more highly developed than those of the Late Palaeolithic. Indeed, fishing took place not only in the receding high waters but also in the main channel of the Nile, which suggests that by this date the people must have been using boats with a reasonable degree of stability. Because of the more humid climate, hunting for aurochs, dorcas gazelle, and barbary sheep was possible in the wadi area. The Elkabian industry is microlithic, including a large number of microburins. It is readily comparable with the Early Neolithic of the Western Desert. The presence of numerous grinding stones cannot be used as evidence for plant processing, because red pigment was still visible on a number of them. The presence of an Elkabian occupation in the Tree Shelter site at Wadi Sodmein, near Quseir in the Eastern Desert, suggests that the Elkabians should be viewed as nomadic hunters, following east-west routes with wintertime fishing and hunting in the Nile Valley and exploitation of the desert during the wet summer.
The Qarunian is a renaming of the Faiyum B culture (attributed by Caton-Thompson to the Mesolithic). Qarunian sites, originally located on high ground overlooking the Proto-Moeris Lake (which dates to about 7050 BC), have been identified in the area north and west of the present Faiyum lake. The Holocene history of the lake is characterized by a number of fluctuations, which are of the utmost importance for the understanding of the history of occupation around the lake. There were three transgressions (that is, submergences of land caused by rises in sea level) preceding the Neolithic. In the Qarunian phase, fishing conditions were exceptionally good in the shallow waters of the lake and it comes as no surprise that fish provided the basis of subsistence. In addition, hunting and food gathering were practised. The Qarunian industry is also microlithic and fits in with the general technological context of the Elkabian and the Early Neolithic of the Western Desert. A single burial is known for the Qarunian. The body of a woman aged about 40 was buried in a slightly contracted position, on the left side, head to the east, facing south. Her physical characteristics are far more modern than the Late Palaeolithic Mechtoids.
The presence of microlithic industries in the neighbourhood of Helwan has been known since the nineteenth century, showing similarities with the Pre-Pottery Neolithic from the Levant, but the real significance of these industries cannot be determined because of the poor information available. Also in the Eastern Desert, in the Red Sea mountains, there are Neolithic settlements. According to the evidence from Sodmein Cave near Quseir, these settlers would have introduced domesticated sheep/goat during the first half of the sixth millennium bc.