By reducing the number of seedlings using marker-assisted selection (MAS), field breeders of cassava can allocate their limited phenotyping resources to a smaller number of selection candidates for further phenotypic evaluation of complex traits such as yield and drought tolerance. This chapter describes the strengths and limitations of MAS, the resources that are required, and outlines the practical considerations for its implementation. The chapter also describes the contribution of genome-wide studies (GWAS), summarizes the published quantitative trait loci (QTL) studies in cassava and looks ahead to future research and developments in this area.