The effective population size (Ne) quantifies the effectiveness of genetic drift in finite populations. When generations overlap, theoretical expectations for Ne typically assume that the sampling of offspring genotypes from a given individual is independent among successive breeding events, even though this is not true in many species, including humans. To explore the effects on Ne of nonindependent mate pairing across breeding events, we simulated the genetic drift of mitochondrial DNA, autosomal DNA, and sex chromosome DNA under three mating systems. Nonindependent mate pairing across breeding seasons has no effect when all adults mate pair for life, a small or moderate effect when females reuse stored sperm, and a large effect when there is intense male–male competition for reproduction in a harem social system. If adult females reproduce at a constant rate irrespective of the type of mate pairing, the general effect of nonindependent mate pairing is to decrease Ne for paternally inherited components of the genome. These findings have significant implications for the relative Ne values of different genomic regions, and hence for the expected levels of DNA sequence diversity in these regions.