Cytoplasmic incompatibility between arthropods infected with different strains of Wolbachia has been proposed as an important mechanism for speciation. However, a basic requirement for this mechanism is the coexistence of different strains in neighbouring populations. Here we test whether this required coexistence is possible in a spatial context. Continuous-time models for the behaviour of one and two strains of Wolbachia within a single well-mixed population demonstrate the Allee effect and founder control, such that one strain is always driven extinct. In contrast, discretised spatial models show patchy persistence of the two strains although coexistence within the same habitat is rare. A simplified model of such founder control suggests that it is fragmentation of (or barriers within) the habitat rather than space itself that leads to persistence.