Purple-fleshed sweetpotatoes (PFSP) can be a healthy food choice for consumers and a potential source for natural food colorants. This study aimed to identify anthocyanins and anthocyanidins in PFSP, and to evaluate the effect of thermal processing on these polyphenolic compounds. Freeze-dried powder of raw and steamed samples of three PFSP varieties were extracted with acidified methanol using a Dionex ASE 200 accelerated solvent extractor. Seventeen anthocyanins were identified by HPLC-DAD/ESI-MS/MS for Stokes Purple and NC 415 varieties with five major compounds: cyanidin 3-caffeoylsophoroside-5-glucoside, peonidin 3-caffeoylsophoroside-5-glucoside, cyanidin 3-caffeoyl-p-hydroxybenzoylsophoroside-5-glucoside, peonidin 3-caffeoyl-p-hydroxybenzoyl-sophoroside-5-glucoside, and peonidin-caffeoyl-feruloylsophoroside-5-glucoside. Okinawa variety showed 12 pigments with 3 major peaks identified as cyanidin 3-caffeoylsophoroside-5-glucoside, cyanidin 3-(6'',6'''-dicaffeoylsophoroside)-5-glucoside and cyanidin 3-(6''-caffeoyl-6'''-feruloylsophoroside)-5-glucoside. Steam cooking had no significant effect on total anthocyanin content or the anthocyanin pigments. Cyanidin and peonidin, which were the major anthocyanidins in the acid hydrolyzed extracts, were well separated and quantified by HPLC with external standards. Cyanidin and peonidin, which contribute to the blue and red hues of PFSP, can be simply quantified by HPLC after acid hydrolysis of the anthocyanins.