Many arthropod species are infected by maternally inherited bacteria that induce cytoplasmic incompatibility (CI). CI causes embryonic mortality in offspring when infected males mate with either uninfected females or with females that are infected with a different strain of bacteria. Here, we review theoretical and empirical studies concerning the infection dynamics of CI-inducing bacteria, focusing in particular on the impact of the host population structure on the spread of CI. As different theoretical models have often produced divergent predictions with regard to issues such as the speed of CI spread and the stability of infection polymorphisms, we specifically aim to clarify how the various assumptions concerning population structure that underlie these models affect these predictions. We also discuss several implications of population structure, including the impact of CI on host gene flow reduction and speciation, the evolutionary dynamics of CI and strategies to control insect pest populations by means of CI-inducing microbes.