Candidate gene approaches have been frequently employed in studies of the molecular genetics of Capsicum. Pepper has been an ideal system for this approach due to the combination of its global crop value, its large genome size, and the ability to use comparative approaches to access the information generated from the investments in tomato as a model organism. Tomato and pepper share DNA sequence similarity, conserved synteny and the research goals of understanding and improving disease resistance and fruit size, shape , yield and quality. This chapter will explore the rationale for the candidate gene approach in pepper, case studies and the future outlook for this approach.