Tree-based farming systems are beneficial both for poverty alleviation and environmental conservation. Despite the growing body of literature supporting the benefits of integrating trees on farm,local perceptions play a larger role in the decision-making of smallholder farmers, especially those who have limited access to scientific studies. This paper explores the priority farming systems and tree species of female and male smallholder farmers in Lantapan, Bukidnon, as well as the reasons for their preferences. Using the Analytical Hierarchical Process (AHP), their criteria for crop selectionwere compared and generated weights were used to assess their priority species. Findings showed that financial benefits of farming systems and tree species were the main consideration of both male and female farmers. Although profit maximization and supply of building materials were their main criteria for tree species selection, women and men also considered different aspects of well-being (i.e. regulatory services, food security). Results indicated that both female and male farmers preferred crop-based farms over tree-based farms. In terms of tree species, female farmers highly preferred plantation crops and timber trees, while male farmers favored fruit trees. The findings of the study could be used in crafting a gender-sensitive co- investment scheme that would support the promotion of climate -smart, tree-based agriculture in the area.