The ecology and landscape in Western Europe during the Holocene has been considerably altered by human activity, primarily through the introduction of agriculture. It is known that this has resulted in biodiversity changes, although it has been rarely investigated if there have also been concomitant evolutionary changes in native species. Apodemus sylvaticus has been present in Western Europe prior to the introduction of agriculture, and due to its anthropogenic tendency has not dramatically declined and continues to persist. Micro-mammal species, which have short generation times, can evolve rapidly. The mandibular morphology has also been shown to be highly evolutionarily responsive to functional demands associated with ecological changes, therefore providing a good model for investigating these patterns. A biomechanical model constructed using extant data is used to test the changes in mandibular shape of Apodemus from archaeological material across the Holocene. We predict either a functional mandibular change, or non-functional changes reflecting random drift over time, or alternatively that the inherent versatility in Apodemus feeding biomechanics has allowed it to persist in a drastically altered ecology. These results will provide important data of long-term human effects on the evolution of organisms in altered ecosystems. This perspective may permit predictions on how human activity will continue to alter and affect micro-mammal phenotypes and ecological systems.