Ecological restoration of trees is often constrained by limited knowledge of the biology, propagation and management requirements of individual species. Consequently, restoration initiatives rarely incorporate less well-known species or those that are difficult to source and grow. We describe challenges associated with the restoration of threatened trees in the Araucaria Forest of southern Brazil, and analyse the effectiveness of methods used to define target species, identify seed sources and generate information on the phenology of rare or threatened tree species. A review of secondary data identified 71 rare or threatened taxa as targets for seed collection. We then surveyed 68.7 km of trails in 26 forest remnants, identifying and mapping 1,027 seed-producing trees of 38 species. Surveys confirmed the scarcity of several tree species (including seven species with an abundance of <0.04 individuals per km), and nine species showed no signs of fruiting during 3 years of phenological monitoring. These findings, together with limited knowledge and application of optimal seed collection methods, are significant factors impeding the recovery of these species within their natural habitat. Wider application of the results of this case study could support restoration of the Araucaria Forest with seedlings from a wider diversity of species.