Berberine, palmatine, alizarin, purpurin, indigotin, and indirubin which were the major coloring compounds of Phellodendron bark, madder, and indigo plant were thermally degraded in 100°C oven in liquid dye form and also in silk dyed with five of these pigments. A mixed dye solution of six coloring compounds was prepared in DMSO solution and was thermally degraded for up to 7 days. Silk were dyed using either a mixed dye solution of five dyes or individual dye solutions and each were degraded for 7 and 14 days, respectively, and the dye was extracted from the samples for the HPLC analysis. The concentration of coloring compounds in the degraded samples were analyzed by HPLC-DAD-MS and the color difference (ΔE) of the degraded silk was examined using a spectro-colorimeter. Alizarin and purpurin were more resistance to degradation than other coloring compounds both when in solution form and in silk dyeings. And such result was verified by the color difference measurement of the degraded silk dyed with individual dye solution. The resistance of alizarin and purpurin to thermal degradation was highly likely due to the fomation of fiber-metal-dye chelated complex by alum or iron mordanting before dyeing.