Cytoplasmic incompatibility (CI) is a reproductive incompatibility induced by maternally transmitted bacteria of the genera Wolbachia and Cardinium. In the simplest form of CI, offspring from infected males and uninfected females suffer from increased mortality. However, it has been noted that crosses between males and females carrying different strains of infection are often also incompatible. The evolutionary processes leading to the emergence of new CI-compatibility types are still not resolved. Here, we develop a model that extends previous theoretical approaches by including segregation of bacterial strains during transmission as well as a continuum of breeding systems ranging from inbreeding (complete sib mating) to outbreeding (complete sib-mating avoidance). Our results demonstrate that (1) with segregation of strains, evolution is unlikely to lead to new CI types that co-occur as a double infection with the preexisting one, (2) inbreeding substantially hampers the evolution of new CI types, and (3) outbreeding facilitates the evolution of new CI types. Our model also provides a hypothesis on the evolutionary origin of CI.