This research was aimed to investigate and compare the effectiveness of TLC and GC-MS methods in the analysis of chromophoric substances extracted from madder plant. Alizarin and purpurin 0.3% solution were used as comparative standards; madder extraction was prepared by heating the solution of powdered madder at 80℃, pH 1.5, for 90 min. Best elution solvent for TLC in silica gel plate was toluene:ethyl acetate=9:1, which resulted in red and yellow spots from madder extraction each of which showed R_f values 0.32-0.43 and 0.07-0.11. Although the red spot in particular exhibited similar characteristics as standard purpurin in color, shape, and R_f values, the result was inconsistent throughout different TLC trials. GC-MS analysis showed only small amount of alizarin and no purpurin in the madder extraction. Other chromophoric substance such as 2-furancarboxaldehyde, 5-(hydroxymethyl)-, anthralin, and danthron were also detected in small amounts. The result indicated that TLC was less sensitive to detecting and identifying the natural dyestuff which is generally constituted with a number of similar but chemically different chromophoric substances.