Hedyotis diffusa Willd. and Hedyotis corymbosa (L.) Lam. are closely related species of Rubiaceae family and they can be easily confused. Although previous reports have been found in which ultraviolet spectrum, convolution spectrometry or X-ray diffraction are reported to be used for distinguishing between the two species, these methods require specialised equipment. Hence, this study aims to develop a simple chromatographic method for the purpose. Our results illustrate the use of a thin-layer chromatographic (TLC) profile to differentiate between the two species, with a blue zone appearing at around an R(f) of 0.36 in H. corymbosa but not in H. diffusa. The compound corresponding to this blue zone was later found to be hedyotiscone A. LC-MS with multiple reaction monitoring was used as a tool to identify and quantify hedyotiscone A in the test samples. In conclusion, a quick and simple TLC assay was conducted to distinguish between the two species H. diffusa and H. corymbosa.