While the health benefits of antioxidant compounds from terrestrial plants are widely accepted in Western counties, there is less recognition of the health benefits of marine algal antioxidant compounds. Oceans are an abundant source of biomaterials, with many natural antioxidants derived from marine algae being investigated as potential anti-aging, anti-inflammatory, anti-bacterial, anti-fungal, cytotoxic, anti-malarial, anti-proliferative, and anti-cancer agents. The aim of this work was to quantify and compare polyphenolic content and free radical scavenging activity of algal extracts using normal phase and reverse phase thin layer chromatography. Post-chromatographic derivatization with neutral ferric chloride (FeCl3) solution and with 2,2-diphenyl-1-picrylhydrazyl (DPPH·) free radical were used to assess total polyphenolic content and free radical scavenging activities in algal samples. Total phenolic content quantified on normal phase plates was correlated to phenolic content established on reverse phase plates. Similarly, free radical scavenging activity established on normal phase and reverse phase plates were in good agreement. However, although free radical scavenging activities determined on normal phase plates were highly correlated with polyphenolic content, this correlation was low for reverse phase plates. Lipophilic reversed phase TLC plates do not effectively separate mixtures of highly polar compounds like flavonoids, phenolic compounds and their glucosides. Thus, although reversed phase plates are recommended for assessment of free radical scavengers, as they do not influence the free radical-antioxidant reaction, they may not provide the best separation of polar phenolic compounds, especially flavonoids, and therefore may not accurately quantify polyphenolic content and free radical scavenging potential.