Genetic diversity analyses, coupled with ecological niche modelling ( ENM) of species with a restricted distribution, may provide valuable information for understanding diversification patterns in endangered areas. We analyzed the genetic diversity of Recordia reitzii, a tree restricted to the threatened and highly fragmented Brazilian Atlantic forest, using three intergenic cpDNA spacers and ten microsatellite ( SSR) loci. To assess the historical processes that may have influenced the distribution of extant R. reitzii populations, the current potential distributions of R. reitzii and Recordia boliviana, a closely related species, were modelled and projected onto the Last Glacial Maximum ( LGM) and Last Interglacial ( LIG) periods. Niche divergence was quantified between these two. The cpDNA and SSR data showed a north-south pattern of the diversity distribution and structured populations, suggesting that gene flow is probably limited. According to our data, R. reitzii exhibits low genetic diversity, which may be a result of a founder or distribution-reduction effect, narrow distribution or small population size. The ecological niche models showed a wider palaeodistribution during the LIG and a retraction during the LGM for both species. Tests of niche divergence and conservatism indicated that bioclimatic factors might have influenced the diversification of these Recordia species. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 332-348. [ABSTRACT FROM AUTHOR]