Chili pepper (Capsicum annuum L.) cv. Árbol and Uvilla fruits differing in anthocyanin contents were analyzed to characterize the accumulation patterns. The maximum accumulation of the aglycon delphinidin occurred 20 days postanthesis (DPA) with higher content in Uvilla than in Árbol fruits. Regarding the cDNA library, 9 186 cDNA clones were selected. The clones with high homology to genes concerning anthocyanin biosynthesis, such as encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonoid 3′,5′-hydroxylase (F3′5′H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), UDP Glc-flavonoid 3-O-gluco-syl transferase (UFGT), and also those possibly involved in anthocyanin transport into the vacuoles, an anthocyanin permease (ANP) and a glutathione S-transferase (GST) were used for gene expression analysis. In general, the expression of all investigated genes was developmentally regulated in both Árbol and Uvilla. CHS and CHI transcripts were expressed at the maximal level at 10 DPA, and then consistently declined throughout fruit development. F3′5′H, DFR, UFGT and GST expression exhibited a positive correlation with anthocyanin accumulation, and the highest transcript levels were detected prior to or by the time of maximum anthocyanin accumulation, depending on the chili pepper type. Pericarp fruit tissues from cv. Tampiqueño 74, an anthocyanin non-accumulator, also showed CHS, CHI, F3H, ANS and ANP expression at some developmental stages.