The house mouse (Mus musculus), after humans, is the most widespread mammal on earth and one of the worst invasive species for both biological diversity and human health. This ubiquity is the consequence of its strong ecological relationship with humans, namely commensalism. Human activities promote its diffusion by eliminating ecological barriers and by increasing the human environment suitable for this species. This paper deals with recent zooarchaeological data that has helped to decipher the main factors of human evolution involved in the origin of commensal behaviour in the house mouse and in its invasive process throughout the Mediterranean. Understanding this process contributes to our overall knowledge on how human activities modelled mammalian diversity during Holocene. In the Near Eastern core of European Neolithisation, two factors are recognised as the main driving forces to explain the beginning of house mouse commensalism: rise of farming practices (cultivated fields, large scale grain storage, domestication of plants) and human dispersal of domesticated plants through the cultural area of the pre-ceramic Neolithic. These factors increased the attractiveness of the anthropic ecosystem as well as the diffusion vectors of mice by passive transport. Nevertheless, the Neolithisation of the Mediterranean did not promote the house mouse's invasion of Europe. The commercial and demographic expansions of Phoenicians and Greeks during the last millennium BC were the vectors that allowed the house mouse to overwhelm the ecological barriers that previously prevented its westward invasion of the human environment.