The transition to food production, exploitation of 'secondary' products (e.g., milk), and advances in cookware technology have affected all aspects of human life. The aim of the present study was to follow changes in mandibular form and shape throughout the terminal Pleistocene-Holocene Levant. The hemimandibles of four populations were included in this study: Natufian hunter-gatherers (n = 10), Pre-pottery Neolithic early farmers (n = 6), Chalcolithic farmers (n = 9), Roman-Byzantine (n = 16), and modern (n = 63) populations. A surface mesh of each mandible was reconstructed from CT or surface scans. Changes in mandibular form and shape were studied using the Procrustes-based geometric morphometrics method. Univariate and multivariate analyses were carried out to examine differences in size and shape between the studied populations. Our results reveal considerable temporal changes in mandibular shape throughout the Holocene Levant, mainly between the pre-agricultural population (the Natufian) and the succeeding ones, and between the post-industrial (the Modern) and the pre-industrial populations. A tendency for a reduction in mandibular size was identified between the pre-agricultural population and the farmers. Most regions of the mandible underwent shape changes. In conclusion, substantial changes in mandibular shape occurred throughout the Holocene Levant, especially following the agricultural revolution. These changes can be explained by the "masticatory-functional hypothesis".