Abstract <p>The neutral genetic diversity (cytochrome <i>b</i> gene and 12 microsatellite loci) was assessed for populations of the semi-commensal species striped field mouse (<i>Apodemus agrarius</i> Pallas, 1771) in five parks of Moscow located in areas with different degrees of urbanization and in two suburban locations in the Moscow Region. It is shown that the most genetically isolated population is the one which represents a distinct genetic cluster with a reduced level of diversity and is revealed from the park located closer to the city center (Neskuchny Garden). The level of genetic differentiation among populations inhabiting other city parks was much lower. This pattern differs from from that previously observed for the allelic diversity of the adaptively significant exon 2 of the DRB gene (MHC). It is assumed that the rate of accumulation of changes in neutral genes is significantly lower than that for genes responsible for the formation of adaptations, for example, to a parasitic load. The data obtained on the genetic diversity of the striped field mouse in Moscow suggest that the condition of city populations of the species more closely aligns with the “urban facilitation” model, rather than the “urban fragmentation” model (according to Miles et al., 2019). Given this, as well as the potential epidemiological risks, it is important to pay attention to the need for ongoing monitoring of urban striped field mouse populations in Moscow and other cities where this species inhabits.</p>