To establish the fingerprint profile of Lobophora variegata using high performance thin layer chromatography (HPTLC) technique. HPTLC studies were carried out using CAMAG HPTLC system equipped with Linomat V applicator; TLC scanner 3, Reprostar 3 and WIN CATS-4 software were used. HPTLC finger printing of methanolic extract of Lobophora variegata revealed 9 peaks with Rf values in the range of 0.18 to 0.86. It can be concluded that HPTLC fingerprint analysis of methanolic extract of Lobophora variegata can be used as a diagnostic tool for the correct identification of the alga and it is useful as a phytochemical marker and also a good estimator of genetic variation in algal populations.