The pandemic distribution of Wolbachia (alpha-proteobacteria) across arthropods is largely due to the ability of these maternally inherited endosymbionts to successfully shift hosts across species boundaries. Yet it remains unclear whether Wolbachia has preferential routes of transfer among species. Here, we examined populations of eight species of the North American funnel-web spider genus Agelenopsis to evaluate whether Wolbachia show evidence for host specificity and the relative contribution of horizontal vs. vertical transmission of strains within and among related host species. Wolbachia strains were characterized by multilocus sequence typing (MLST) and Wolbachia surface protein (WSP) sequences, and analysed in relation to host phylogeny, mitochondrial diversity and geographical range. Results indicate that at least three sets of divergent Wolbachia strains invaded the genus Agelenopsis. After each invasion, the Wolbachia strains preferentially shuffled across species of this host genus by horizontal transfer rather than cospeciation. Decoupling of Wolbachia and host mitochondrial haplotype (mitotypes) evolutionary histories within single species reveals an extensive contribution of horizontal transfer also in the rapid dispersal of Wolbachia among conspecific host populations. These findings provide some of the strongest evidence to support the association of related Wolbachia strains with related hosts by means of both vertical and horizontal strain transmission. Similar analyses across a broader range of invertebrate taxa are needed, using sensitive methods for strain typing such as MLST, to determine if this pattern of Wolbachia dispersal is peculiar to Agelenopsis (or spiders), or is in fact a general pattern in arthropods.