Speciation in brood-parasitic indigobirds (genus Vidua) is a consequence of behavioural imprinting in both males and females. Mimicry of host song by males and host fidelity in female egg laying result in reproductive isolation of indigobirds associated with a given host species. Colonization of new hosts and subsequent speciation require that females occasionally lay eggs in the nests of novel hosts but the same behaviour may lead to hybridization when females parasitize hosts already associated with other indigobird species. Thus, retained ancestral polymorphism and ongoing hybridization are two alternative explanations for the limited genetic differentiation among indigobird species. We tested for genetic continuity of indigobird species using mitochondrial sequences and nuclear microsatellite data. Within West Africa and southern Africa, allopatric populations of the same species are generally more similar to each other than to sympatric populations of different species. Likewise, a larger proportion of genetic variation is explained by differences between species than by differences between locations in alternative hierarchical amovas, suggesting that the rate of hybridization is not high enough to homogenize sympatric populations of different species or prevent genetic differentiation between species. Broad sharing of genetic polymorphisms among species, however, suggests that some indigobird species trace to multiple host colonization events in space and time, each contributing to the formation of a single interbreeding population bound together by songs acquired from the host species.