Fleshy fruits in different species can display large variation in color. A link between fruit color and seed dispersal success is suggested by previous studies showing that high intensity of fruit color increases the visitation rate in seed-dispersing birds. Wild tomato species (Solanum spp.) are excellent model organisms for research on genetic basis of differential fruit color development during the ripening process. Despite polymorphism in fruit color, all tomato species have yellow flowers due to accumulation of carotenoid pigments, which suggests that the carotenoid pathway is intact. Thus, regulatory changes controlling enzymes activity during fruit maturation are likely to have played a role in fruit color evolution. Our transcriptome analysis of wild tomato species revealed that differences in cyc-b and crtr-b2 expression could explain the diversity of fruit color. Additionally, co-expression analysis elucidated regulators of the carotenoid pathway. Combined with Sanger sequencing of carotenoid pathway genes, we identified genes that may underlie differences in fruit color during tomato evolution.