Two chromosomal races of the house mouse occur in Tunisia, a standard morph (40St) found all over the country, and a derived morph (22Rb) occurring only in central Tunisia. In this region, habitat partitioning between the two morphs was investigated by a microgeographical analysis of their distribution, assessing habitat characteristics and demographic parameters. Results showed that the 22Rb mice always occurred in the oldest sections of towns (medinas), often extending to more recent surrounding neighbourhoods where the 40St morph was most abundant. The latter was never trapped within the medinas. The transition between the two morphs was located within cities in the more recent areas, the hybrid zone being estimated at less than 0.5 km in width by a clinal analysis of chromosomal data. Although differences between habitats exist, almost no demographic differences were found between populations of the two morphs when they occurred in the same or in different habitats. Two hypotheses are discussed to account for the origin of habitat partitioning. The first relies on competitive exclusion of the 40St mice from the medinas by the derived 22Rb mice; the second is based on stochastic processes related to historical evolution of Tunisian urban communities.