Annatto (Bixa orellana) is the sole source of the commercially important pigment bixin. The broad diversity of annatto phenotypes and the wide variation in pigment contents have restricted its use. Therefore, genetic improvement focusing on this variation is important in order to achieve optimal exploitation of annatto. To characterize and understand some of the genetic basis governing carotenoid production, two annatto cultivars with either pink or white flowers were selected on the basis of their contrasting pigment levels. Several complementary DNA (cDNA)-probes corresponding to genes involved in carotenoid biosynthesis (dxs, psy, pds, β-lcy, and ε-lcy) were cloned and analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR) in different tissues of these two annatto cultivars during flower and fruit development. In general, expression of most selected genes could be associated with pigment overaccumulation in these cultivars. The pink cultivar exhibited higher carotenoid contents and higher pigment-related gene expression, and the two variants analyzed showed notable differences in gene expression in the highest pigment producing tissues.