Pumpkin and squash are widely utilized across various industries, including culinary, ornamental, snacking, and seed oil production. Despite their substantial genetic diversity, productivity and genetic improvement in these crops are constrained by several factors, including auxiliary traits, notably the emergence of new insect pests, pathogens, and abiotic stresses driven by climate change, as well as the growing demand for nutritious food. These challenges have necessitated a shift in breeding objectives and methodologies. Conventional breeding alone is insufficient to meet the increasing global demand, exacerbated by population growth, resource depletion, and plateauing yield trends. Consequently, the future of pumpkin and squash breeding lies in integrating traditional breeding techniques with advancements in bioinformatics and molecular biology, which can enhance the efficiency of breeding programs by predicting and estimating genetic variations linked to desirable phenotypic traits. Two promising approaches that can significantly advance modern breeding efforts are genome-wide association studies (GWAS) and the mapping of quantitative trait loci (QTL) for traits of interest, both of which are crucial for ensuring food and nutrition security. In this chapter, we critically examine how these techniques have been applied to squash breeding, highlighting their challenges and prospects.