Soils with toxic levels of boron (B) are widespread in the cereal-livestock zone of southern Australia. The annual pasture legume burr medic (Medicago polymorpha L.) is widely grown in rotation with grain crops in this zone, but current cultivars are susceptible to high levels of B. We tested the boron tolerance of several putative B tolerant burr medic accessions and developed four F₂ populations by crossing two tolerant accessions with two susceptible cultivars. We tested a B tolerance SSR marker developed for barrel medic (M. truncatula Gaernt) on tolerant burr medic accessions but found a new marker was required. We identified several B tolerant burr medic accessions. In our four F₂ populations tolerance was inherited in a 3 : 1 (tolerant : susceptible) ratio and we identified a molecular marker that accounts for 0.84 of the variation. The B tolerant accessions, along with the B tolerance marker, will allow for the efficient introgression of B tolerance into widely adapted genetic backgrounds and will allow breeders to efficiently develop cultivar(s) that are tolerant of a widespread subsoil constraint.