Brazilwood (Caesalpinia echinata Lam) is a tree native to the Atlantic rainforest. It has been exploited since the Brazilian colonial period and the remaining natural populations of C. echinata have been reduced to small forest fragments, or are conserved in arboreta and ecological parks. This study aimed to identify the degree of genetic diversity present within brazilwood trees from three different sites in southern Bahia State, through random amplified polymorphic DNA (RAPD) markers and discuss criteria to enrich an ex situ conservation area in the campus of the Universidade Estadual de Santa Cruz, Brazil. Out of the 53 primers tested, 16 revealed 38 reproducible polymorphic and good quality bands. The similarity coefficients among individuals varied from 0.43 to 1.00. The average similarity coefficients were higher in ex situ collections (0.82 to 0.70) than in situ region (0.46). The UPGMA analysis displayed the formation of three distinct groups, although the similarity among all accessions was high (around 70%). The conservation of plant species away from their natural habitat needs to be done carefully, with the introduction of individuals that offer the highest level of genetic diversity possible and contribute to the biological preservation of the species.