This paper presents some recent interdisciplinary advances in the study of ancient agriculture in Egypt and Sudan through the lens of palaeoethnobotany. It will engage with the rich tradition of the study of crop selection of the region, looking at longue durée changes from the mid-2nd millennium B.C. until the late Islamic period through a series of case studies from the authors’ own archaeological sites. It will also briefly reflect on some of the first results of biochemical analyses of ancient cereals and pulses from Roman Karanis.