The leaves of Hibiscus sabdariffa L. are one of the sources of food and traditional medicine. A combination of high-performance thin-layer chromatography (HPTLC) bioautographic assay with mass spectrometry (MS) has been performed to screen and identify the antioxidant compounds in the leaves of H. sabdariffa L. The crude extract of H. sabdariffa L. was separated on silica gel 60 HPTLC plates in an automatic developing chamber (ADC2) with toluene–ethyl acetate–formic acid–methanol (6:6:1.6:1, v/v) as the mobile phase. Antioxidant bands were visualized by dipping in 2,2-diphenyl-1-picrylhydrazyl (DPPH) reagent. Five antioxidant compounds were identified as neochlorogenic acid (1), chlorogenic acid (2), cryptochlorogenic acid (3), rutin (4), and isoquercitrin (5), which could be the predominant contributors to the antioxidant activity of the leaves of H. sabdariffa L. Furthermore, principal component analysis (PCA) was carried out to discriminate ten accessions of H. sabdariffa L. using an image-processing software. This simple HPTLC fingerprint assisted by PCA can be used as a reliable method for the discrimination of different accessions of H. sabdariffa L.