In Indian system of medicine, Eclipta prostrata is an important herbal ingredient of several Ayurvedic and Siddha formulations and it is commonly called as Bhringraja. But, this plant is often confused with Wedelia calendulacea, which is also known as Bhringraja and also being adulterated in Indian herbal market. In order to differentiate these plant drugs (Eclipta prostrata and Wedelia calendulacea), in the present work we have developed chemical fingerprints. Phytochemical analysis, UV-Visible, FT-IR and NMR spectroscopy, HPTLC and HPLC chromatography were carried out in the selected plant materials. Phytochemical analysis of methanolic extract of investigated materials showed that W. calendulacea contained higher level of total phenolic compounds (381.82 mg GAE/100 g) when compared to E. prostrata (105 mg GAE/100 g). Scanning in UV-Visible spectroscopy exhibited difference between selected samples, especially at 250-450 nm. Similarly, FT-IR spectroscopy of raw materials indicated notable difference between the samples at 400 -1000 cm -1 region. NMR spectroscopy illustrated remarkable difference between the chloroform extract of selected samples at 1-2 ppm region. HPTLC profile of methanolic extract of E. prostrata exhibited a total number of 9 peaks while W. calendulacea showed 12 number of peaks. Chemical profile investigated in the present study would be helpful to differentiate E. prostrata from W. calendulacea and also useful to prevent their adulteration in herbal industry.