Examples of recurrent homoploid hybrid speciation are few. One often-cited example is Argyranthemum sundingii. This example includes two described species, A. lemsii and A. sundingii, resulting from reciprocal hybridization between A. broussonetii and A. frutescens on Tenerife. The four species and artificial F1 and F2 hybrids have previously been investigated morphologically and cytologically. Here, we examine population differentiation based on amplified fragment length polymorphism to get a better understanding of the genetic relationships among the species and the extent of hybridization. We aim to investigate if there is molecular support for treating the hybrid species as one taxon. Seven parental and four hybrid species populations (149 individuals) were analysed and we scored 85 polymorphic markers. A few (2–5) were private to each species but variably present and mostly rare. Our principal coordinate, STRUCTURE and BAPS analyses and AMOVA resulted in a clear separation of the parental species. The hybrid species were genetically less divergent but not identical. Our data indicate that hybridization and introgression are common in all these species on Tenerife and support the hypothesis that homoploid hybrid speciation has occurred repeatedly. Intrinsic post-zygotic barriers are notoriously weak in Argyranthemum and reproductive isolation and speciation result primarily from strong ecological selection. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 19–31.