Oasis agriculture has been a critical means of sustenance for humans in arid regions in North Africa and West Asia. The date palm ( Phoenix dactylifera L.) holds immense significance as one of the most vital species in these agroecosystems. It was domesticated in the Gulf region over 6000 years ago and later spread to other regions. In the Sahara, the origins of the germplasm and the diffusion history in terms of dating and routes remain largely unknown. To explore these questions, we employed traditional and geometric morphometric methods to analyse 312 well-preserved Phoenix seeds from three Libyan sites, dating from the 1st millennium BCE to the modern period. We compared them with a large modern reference collection and Egyptian archaeological seeds from a previous study. The identification of domesticated morphotypes in the oldest site, Zinkekra, confirms that the date palm was already cultivated in the Central Sahara during the 1st millennium BCE, probably through an introduction from Egypt. The large proportion of wild morphotypes however indicates that they represent early domesticates. By comparing seeds at sites in Libya and Egypt dating from different periods, evidence was found of a decrease in unclassified seeds and wild morphotypes over time, along with a simultaneous increase in seed elongation. These results likely reflect the intensification of date palm cultivation, coinciding with the growing prevalence of human selection and vegetative propagation. Our study highlights the potential of seed morphometric analyses in uncovering the domestication and diffusion history of crops, shedding light on how humans have adapted to challenging environments.