Taro (Colocasia esculenta) is the tropical root crop species featuring the greatest flavonoids diversity. Their quantification is important for breeding programmes focusing on biofortification. This study aims at developing an HPTLC protocol to compare the flavonoids fingerprints of more than 1800 hybrids belonging to 24 full-sib families and to select genotypes with high levels of antioxidants. Twenty different chemical markers were identified based on bands Rf and colour. Flavonoids differ among individuals both quantitatively and qualitatively. Marker 'A' yielded the strongest antioxidant response to DPPH, equivalent to the one with quercetin pure standard. Overall, 377 high flavonoids content (HFC) hybrids were selected from 14 different families. The mean corm weight of HFC hybrids always appeared higher than the mean corm weight of the family they belong to. This method allows unambiguous selection of HFC hybrids. It also contributes to taro genetic improvement for nutritional value and access to new markets and to strengthen corm tolerance to pests and diseases. It could be applied to other tropical root crop species.