Citrus fruits are of great relevance both in economic and health terms. Because of that, great efforts have been paid to understand the complex processes that take place during the ripening of the Citrus fruits, that is responsible of the attractive color, shape and flavor. The appearance of the omics technologies, specially transcriptomics, with RNA-Seq as its main tool, has helped to unveil the regulatory mechanisms involved in Citrus fruit ripening, and to find the genes that control these mechanisms, that have become the targets of the citrus breeding programs.