•Sixty pecan accessions were morphologically, chemically and genetically evaluated.•Morphometric measures presented mean values similar to estimations previously reported.•Chemical composition is near homogeneous among accessions.•Genetic splitting of accessions was not related to other traits, but revealed high diversity.•The retrieved data have suitable application for species breeding and the release of new cultivars. Pecan (Carya illinoinensis) is an important commercially cultivated nut tree grown in several countries around the world, including temperate, tropical and subtropical regions. We employed morphometric, chemical and genetic analyses to characterize 60 pecan accessions from Southern Brazil. Here we show that a large spectrum of morphological traits is conserved in the trees cultivated by local farmers. On the other hand, chemical composition of the accessions did not diverge significantly. In addition, moderate to high genetic diversity is observed in these plants. Based on these results, we suggest the use of Participatory Plant Breeding as strategy for conservation of the genetic resources of pecan and improvement of nut production and commercialization. Moreover, the intellectual property of the farmers responsible for the genetic improvement of pecan have to be recognized and protected, since it is the key factor in this process.