Natural rubber is a strategic raw material in many sectors of modern industrial societies and is almost exclusively produced by cultivating rubber trees [Hevea brasiliensis (Willd. ex A. Juss.) Mull. Arg.)]. Breeding of this species focuses mainly on advanced improved varieties developed over a century in Southeast Asia and Africa, but it also relies on genetic diversity available in wild germplasm. In this study, we describe the diversity observed within 1060 accessions originating from the state of Rondonia (Brazil) and conserved ex situ in Vietnam. Available passport data for these accessions indicate their putative distribution throughout seven districts in Rondonia. Genotyping data obtained on these accessions with 15 SSR markers generated 458 different alleles. A principal coordinate analysis enabled a clear separation of accessions from Calama district on the first axis, as well as accessions from Ariquemes and Ji-Parana districts on opposite sides of the second axis. A three-step Bayesian analysis of population structure gave a clearer representation, involving three levels of differentiation. At the first differentiation level, the accessions were divided into two clusters, k1 comprising 42% of the accessions, k2 with 25%, and the remaining 33% being admixed accessions. Further levels of Bayesian analysis enabled to distinguish between accessions from different farms in a same district. A better knowledge of the genetic structure at the infra-Rondonia state level, will help in using this available genetic diversity in future breeding programs.