Population genetics studies can provide knowledge in support of conservation efforts for plant populations. We studied the genetic diversity and structure in nine populations of Calophyllum brasiliense from Santa Catarina state, Brazil, aiming to establish conservation strategies. Allozymic markers were used to genotype about 50 individuals from each population. Moderate genetic diversity (mean = 0.135) and high fixation indexes (mean = 0.259) were estimated. Genetic divergence was significant, equal to 0.140, and a Bayesian analysis found two different genetic groupings. The results show clear signs of risk of diversity loss, basically related to restrictions of effective size. As conservation efforts, we suggested the use of C. brasiliense in restoration programs and for wood production. We also suggested the protection of its associated fauna and the development of more protected areas. Finally, populations 430, 640, 642 and 913 were indicated as priorities for conservation, based on their genetic indexes.
