We analyse the genetic variability in the yellownecked mouse (Apodemus flavicollis) population in the city of Warsaw, Poland, and its surroundings -a species that has begun to occupy the city only in the last 30 years. We also compare the genetic variability of this species with corresponding data collected in the same time and areas for another species -the striped field mouse (Apodemus agrarius). The results indicate a gradual decrease in genetic diversity and increase in relatedness in the population of A. flavicollis from non-urban locations towards sites with the highest anthropopressure. The genetic structure was more pronounced in the 'recent invader' (A. flavicollis) than in the 'permanent inhabitant' (A. agrarius), which has a much longer city colonization history (more than 100 years). In general, FST was higher in A. flavicollis, which may indicate different and independent ways of city colonization by the species. The process by which urban areas are settled by a new, typically forest-dwelling species such as A. flavicollis, more 'sensitive' to the conditions of life in a city, probably includes not only successful events of penetration of the city by small groups of individuals (the founder effect), but also temporary extinctions of local urban populations of A. flavicollis or at least marked fluctuations in species population numbers. Suitably planned areas at the city borders could play an important role as 'gateways' through which individuals from non-urban populations could migrate into the city and join urban populations.