Hancornia speciosa Gomes is an important species from Brazil, distributed in the Cerrado, Caatinga and Atlantic Rain Forest domains. Six botanical varieties are described for H. speciosa, of which are distributed in different regions, however, currently, only two varieties are recognized (pubescens and speciosa). Additionally the phylogeographic and phylogenetic studies have not been reported for H. speciosa, which only phylogeographic study has been related for populations from the Cerrado domain. Here we aimed to assesses the phylogeographical structure of H. speciosa and build the phylogenetic tree using trnH-psbA sequences from chloroplast genome and six microsatellites loci of nuclear genome. The results for chloroplast sequence showed 11 haplotypes and phylogenetic tree revealed two main clades, which the first clade containing the botanical varieties H. speciosa var gardneri, H. speciosa var pubescens and H. speciosa var cuyabensis and secund clade containing the botanical variety H. speciosa var speciosa. The microsatellite analysis revealed on group containing botanical variety H. speciosa var speciosa, while another group consisted of other botanical varieties. The phylogeographic structure revealed five groups: two corresponded to variety H. speciosa var speciosa (individuals from Caatinga and Atlantic Rain Forest domains) and other three groups contain the botanical varieties H. speciosa var gardneri, H. speciosa var pubescens and H. speciosa var cuyabensis (individuals from Cerrado domain). The genetic structure and phylogenetic data support the two recognized botanical varieties of H. speciosa.

Hancornia speciosa Gomes, a native fruit tree, plays an important socio-economic role in Brazil's traditional communities. The objective was to estimate the genetic structure of 176 individuals from eight locations in the Cerrado, Caatinga and Atlantic Forest biomes, based on six microsatellite markers. The analyzes revealed the formation of five population groups: A-Pernambuco, Paraíba and Sergipe (Atlantic Forest), B-Maranhão (Cerrado); both, var. speciosa, C-Bahia (Caatinga / Cerrado transition zone) and Ceará (Caatinga), D-Goiás (Cerrado) and E-Minas Gerais (Cerrado,) being groups C, D and E possibly var. pubescens. Most of the genetic variation is within the groups (65.61%, Fst = 0.34, p <0.001). Although group A had the highest Ho (0.66), it had a negative fixation index (f = -0.02), while the other had positive values. Our results revealed high levels of genetic diversity and provide support the development of more efficient conservation strategies for H. speciosa.