Abstract Archaeological material adds a temporal dimension to evolutionary studies that is valuable for elucidating long-term population stability and evolutionary shifts for species closely associated with humans. Here, a two-dimensional geometric morphometrics approach on first upper molars was applied to modern and archaeological samples to assess the evolution of house mice in Orkney, an archipelago north of Scotland. Modern populations included localities in Orkney, north Scotland, and France. Two archaeological sites in Orkney represented the Norse period: Birsay Beachview (Mainland) and Tuquoy (Westray) (10th–14th/15th centuries AD). The archaeological specimens were larger than modern specimens from similar settings, suggesting processes leading to a recent decline in the size of Orkney house mice. Molar morphology and associated non-metric traits distinct to the Orkney lineage were already established in the Norse period, as indicated by morphological similarity of the Birsay samples to modern Orkney and north Scotland populations. Stability of human settlement is likely to influence morphological evolution in house mice. The Birsay site, located in Birsay village, which has been inhabited since Norse times, might represent the ancestral house mouse population in Orkney. Tuquoy, a settlement abandoned by the end of the medieval period, provided samples different from modern house mouse populations in Westray and neighbouring isles.