Background and Aims Adansonia comprises nine species, six of which are endemic toMadagascar. Genetic rela- tionships between the Malagasy species remain unresolved due to conflicting results between nuclear and plastid DNAvariation.Morphologically intermediate individuals between distinct species have been identified, indicative of interspecific hybridization. In this paper, microsatellite data are used to identify potential cases of hybridization and to provide insights into the evolutionary history of the genus on Madagascar. †Methods Eleven microsatellites amplified with new primers developed for Adansonia rubrostipa were used to analyse 672 individuals collected at 27 sites for the sixMalagasy species and morphologically intermediate indivi- duals.Rates of individual admixturewere examined using threeBayesian clustering programs, STRUCTURE,BAPS and NewHybrids, with no a priori species assignment. †Key Results Population differentiation was coherent, with recognized species boundaries. In the four Malagasy species of section Longitubae,8.0, 9.0 and 9.5% of individuals with mixed genotypes were identified by BAPS, NewHybrids and STRUCTURE, respectively. At sites with sympatric populations of A. rubrostipa and A. za, NewHybrids indicated these individuals to be F2 and, predominantly, backcrosses with both parental species. In northern Madagascar, two populations of trees combining A. za and A. perrieri morphology and microsatellite alleles were identified in the current absence of the parental species. †Conclusions The clear genetic differentiation observed between the six species may reflect their adaptation to dif- ferent assortments of climate regimes and habitats during the colonization of the island. Microsatellite variation reveals that hybridization probably occurred in secondary contact between species of section Longitubae. This type of hybridizationmay also have been involved in the differentiation of a local newstabilized entity showing spe- cific microsatellite alleles and morphological characters, suggesting a potential role of hybridization in the recent history of diversification on Madagascar