It is demonstrated that the structured coalescent model can readily be extended to include phenomena such as partial selfing and background selection through the use of an approximation based on separation of time scales. A model that includes these phenomena, as well as geographic subdivision and linkage to a polymorphism maintained either by local adaptation or by balancing selection, is derived, and the expected coalescence time for a pair of genes is calculated. It is found that background selection reduces coalescence times within subpopulations and allelic classes, leading to a high degree of apparent differentiation. Extremely high levels of subpopulation differentiation are also expected for regions of the genome surrounding loci important in local adaptation. These regions will be wider the stronger the local selection, and the higher the selfing rate.