Capsicum peppers is one of the most important vegetables, with a well known nutritional properties, including phenolics. Breeding peppers adapted to organic agriculture and rich in bioactive compounds is of paramount importance for this sector since the demand of organic and healthy food is increasing in many countries. This is a preliminary study on the effect of genotype, growing conditions and their interaction on the main phenolics of peppers. Fruits from four Capsicum annuum (BGV-10582, Bierzo, Bola and Piquillo) and one C. chinense (ECU-994) accessions, were cultivated under organic and conventional practices and main phenolic compounds quercetin and luteolin were analysed by high performance liquid chromatography (HPLC). Differences were found among accessions for both compounds in the studied accessions, particularly ECU-994. Differences for each phenolic compound were also detected between growing systems. Moreover, considerable interaction between genotype and growing conditions was found, suggesting that there are ample opportunities for selecting peppers with high content in phenolics and specifically adapted to organic cultivation.