Wolbachia, probably the most common animal endosymbiont, infects a wide range of arthropods as well as filarial nematodes. Generally vertically transmitted from mothers to offspring, it has evolved various strategies, ranging from brutal male-killing to mutualism, which facilitate invasion and persistence of the infections within host populations. Current interest in Wolbachia as a potential control agent against harmful nematodes and arthropods makes it important to be able to predict Wolbachia epidemiology and evolutionary trajectory. Here we highlight recent theoretical developments and suggest future modelling and empirical directions for basic and applied research in this domain.