The invention provides methods and compositions for breeding pepper (Capsicum sp. such as Capsicum annuum) lines, including isogenic and nearly isogenic lines, displaying one or more mature fruit color(s) of interest. Predictive genetic markers and associated sequences and primers, associated with phenotypic diversity at the Ccs locus encoding Capsanthin-Capsorubin Synthase, and the Ze locus encoding Zeaxanthin Epoxidase are also provided, as well as methods for breeding pepper lines. Further provided are pepper plants, and plant parts including seeds, seed mixtures, fruit, and packaged fruit, which display mature fruit color(s) of interest.