The colored material (X) was effectively separated from sugarcane molasses using reversed-phase chromatography. Characterization of the molecular structure of sample X was performed using infrared absorption (IR) spectrometry, mass spectrometry (MS), and dynamic light scattering (DLS). The IR spectrum was similar to that of commercial humic acid, and the MS analysis showed that the sample possessed relatively small heterogeneous molecules with molecular masses around 234, 446, 657, 868, and 1079 Da. On the other hand, X sample showed an inhibitory activity toward the cysteine proteinase papain. Furthermore, the inhibitory (G-1) and weak inhibitory (G-2) fractions were separated from sample X using gel permeation chromatography. Samples G-1 and G-2 inhibited papain partial-noncompetitively and had the inhibition constants of 5.01 x 10(-5) and 1.08 x 10(-3)M, respectively. Interestingly, in the DLS experiment, the Stokes radius of sample G-1 was approximately 2 nm, about twice one of sample G-2.