Faunal evidence from the Fayum Neolithic is often cited in the framework of early stock keeping in Egypt. However, the data suffer from a number of problems. In the present paper, large faunal datasets from new excavations at Kom K and Kom W (4850–4250 BC) are presented. They clearly show that, despite the presence of domesticates, fish predominate in the animal bone assemblages. In this sense, there is continuity with the earlier Holocene occupation from the Fayum, starting ca. 7350 BC. Domesticated plants and animals appear first from approximately 5400 BC. The earliest possible evidence for domesticates in Egypt are the very controversial domesticated cattle from the 9th/8th millennium BC in the Nabta Playa-Bir Kiseiba area. The earliest domesticates found elsewhere in Egypt date to the 6th millennium BC. The numbers of bones are generally extremely low at this point in time and only caprines are present. From the 5th millennium BC, the numbers of sites with domesticates dramatically increase, more species are also involved and they are usually represented by significant quantities of bones. The data from the Fayum reflect this two phase development, with very limited evidence for domesticates in the 6th millennium BC and more abundant and clearer indications in the 5th millennium BC. Any modelling of early food production in Egypt suffers from poor amounts of data, bias due to differential preservation and visibility of sites and archaeological remains, and a lack of direct dates for domesticates. In general, however, the evidence for early stock keeping and accompanying archaeological features shows large regional variation and seems to be mainly dependent on local environmental conditions. The large numbers of fish at Kom K and Kom W reflect the proximity of Lake Qarun.