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Tropical tree species complexes harbour closely related species that display shared alleles and that are difficult to delimit using phylogenetic approaches. Such species complexes arise when lineage sorting is slow due to large effective population sizes typical in trees, when diversification is accompanied by interspecific gene flow, or due to a combination of both processes. The concerned species are often difficult to distinguish morphologically due to high phenotypic trait variation. The large intraspecific variation typical of tree species complexes promotes adaptive processes, suggesting that species complexes are important in the diversification of tropical tree biodiversity. The evolutionary histories of these systems remain however poorly understood. We here investigated the evolutionary history of tropical tree species complexes by examining the phylogeny and population genetic processes in sympatric taxa of the Bertholletia clade (Brazil nut clade, Lecythidaceae) in French Guiana. We sampled 192 individuals belonging to 26 tree species of the Bertholletia clade and sequenced them at nine plastid, eight mitochondrial and 134 putative nuclear loci derived from double-digest restriction site associated DNA sequencing (ddRAD-Seq). Phylogenetic methods recovered the expected large sub-clades within the Bertholletia clade, but genetic clustering methods were needed to delimit species within these clades. Some common species such as Eschweilera coriacea, harboured several sympatric gene pools, indicative of hitherto undescribed cryptic species. Outlier detection methods revealed that few single nucleotide polymorphisms (SNPs) were strongly diverged among gene pools, whereas a significant portion of SNPs was more shared than expected a priori in sympatric populations. The local pattern of allele sharing pointed to hybridization, rather than incomplete lineage sorting. Taken together, our results suggest that hybridization is important for adaptive evolution in tropical tree species complexes.