Cytoplasmic incompatibility (CI) induced by intracellular bacteria is a possible mechanism for speciation. Growing empirical evidence suggests that bacteria of the group Wolbachia may indeed act as isolating factors in recent insect speciation. Wolbachia are cytoplasmically transmitted and can cause uni- or bidirectional CI. We present a mainland-island model to investigate how much impact Wolbachia can have on genetic divergence between populations. In the first scenario we assume that the island population has diverged at a selected locus and ask whether genetic divergence will be maintained after introduction of migration from the mainland. In the second we explore whether divergence will originate under migration. For simplicity, the host organisms are modeled as haploid sexuals. Simulations show that if each population is initially infected with a different strain of Wolbachia, then higher levels of divergence occur at the locally selected locus than in the absence of Wolbachia. A weaker effect is seen when there is only unidirectional CI caused by a single strain of Wolbachia on the island. CI increases divergence because it reduces effective migration between mainland and island. Migrants suffer from being confronted with the wrong CI system and this also applies to their matrilineal descendants. Moreover, there is a strong linkage disequilibrium between host genotype and infection state, which helps to maintain Wolbachia differences between the populations in the face of migration A sex bias in migration can either increase or decrease the effect of Wolbachia on divergence. Results support the view that Wolbachia has the potential for increasing divergence between populations and thus could enhance probabilities of speciation.