The isolation and chemical characterization of yellow food pigments from Monascus purpureus were studied according to the compositions of media. Monacus yellow pigments were isolated and purified by solvent fractionation, silicagel column chromatography, TLC and HPLC. The retention time of Monascus yellow pigments isolated by HPLC was respectively 5 min(I) and 9 min(II) as the yeast malt extract agar(YMA) media and was respectively 4.6 min(III), 5 min(I) 5.7 min(IV), 8.3 min(V), 9 min(II) and 10.7 min(Ⅵ) at the malt extract agar(MEA) media. The structure of monascin(I), ankaflavin(II), 6,11-dihydrorubropunctatin(III), 6,11-dihydromonascorubrin(V) and unknown compounds(IV,Ⅵ) was elucidated by EI-Mass, H and C NMR, UV-visible spectrometer. Therefore, it was suggested that 6,11-dihydrorubropunctatin(III) and 6,11-dihydromonascorubrin(V) are new intermediates of Monascus yellow pigments.