Extra-pair paternity (EPP) is an important component of avian mating systems and can affect avian biodiversity by contributing to isolation between related forms. Over the past three decades, molecular surveys of more than 100 species have revealed EPP to be widespread in socially monogamous birds, significantly increasing the variance in reproductive success among males and helping to drive sexual selection on traits with which it is often associated (e.g. song, ornamental plumage). In the past 7 years many studies have also demonstrated that the distribution of EPP within a population is related to the level of genetic similarity between the parents. Multiple mating combined with sperm competition that follows a genetically loaded raffle model, would provide a route through which females could target compatible genes and act as an effective post-copulatory isolating mechanism between closely related species or forms in sympatry. EPP can result in significant divergence between an observed social mating system and the true underlying genetic mating system of a population or species, and needs to be considered in our attempts to define and understand species or morphs as genetically isolated populations in many cases.