Habitat fragmentation, the process by which continuous habitats are broken into smaller, isolated patches, can alter gene flow between species and thereby influence their hybridization and the resulting exchange of genetic material through introgression. This study used spatially explicit simulations to assess how different configurations of habitat fragmentation affect the extent and spatial distribution of introgression between two interacting species. We tested five scenarios varying in carrying capacity, duration of hybridization, expansion dynamics and species spatial overlap. In all scenarios where both species coexist over the full landscape, fragmentation alone has no consistent effect on mean introgression and its spatial variance. However, when contact was restricted to discrete zones, the length of contact areas and the intensity of local hybridization has a clear influence on introgression levels. These results suggest that fragmentation impacts introgression primarily through its effect on the spatial structure of species interactions. This highlights the importance of incorporating spatial dynamics into conservation strategies, particularly in hybrid zones within fragmented habitats.