After its near eradication in the 1940s, the common bed bug (Cimex lectularius) experienced a global resurgence. Within a few years after, some populations displayed insecticide resistance. Two distinct lineages of bed bugs were identified, each associated with humans and bats, respectively. A strong genetic differentiation was identified between bugs from human and bat sites across Europe. This raises the question of whether the same pattern is found at a local scale. Moreover, because long-distance dispersal of bed bugs is essentially human-mediated, we investigated the spread of bed bugs within and among sites. Using mitochondrial (cytochrome oxidase unit I (COI) and 16S rRNA genes) and nuclear (10 microsatellite loci) markers, we compared the genetic composition of human- and bat-associated bed bugs from western Switzerland. We first conducted a median-joining analysis and compared it to European sequences to detect local-scale host-specific separation of haplotypes. We estimated levels of genetic diversity and structure between and within the two host-associated bed bugs. Our results reveal two genetic clusters associated with bats and humans and a strong structure among human sites (F _SC = 0·579). An analysis of knock-down insecticide resistance gene variants (V419L, L925I, I936F) shows that bed bugs infecting humans in western Switzerland carry insecticide resistance (99%) whereas bed bugs infecting bats do not (0%). Our results show that at the scale of western Switzerland, bed bugs are structured by host association, thus supporting the hypothesis of host specialization in the common bed bugs. Moreover, human-associated bugs might have settled from multiple colonization events and/or undergone bottlenecks.