Application of natural resources from the marine environment in the cosmeceutical industry is gaining great attention. This study pursues to discover the cosmeceutical potential of two Malaysian algae, Sargassum sp. and Kappaphycus sp. by determining their antioxidant capacity and assessing the presence of their secondary metabolites with cosmeceutical potential using non-targeted metabolite profiling. Metabolite profiling using Quadrupole Time-of-Flight (Q-TOF) liquid chromatography-mass spectrometry (LC-MS) in the Electrospray Ionization (ESI) mode resulted in 110 putative metabolites in Sargassum sp. and 47 putative metabolites in Kappaphycus sp. and were grouped according to their functions. To the best of our knowledge, the bioactive compounds of both algae have not been studied in any great detail. This is the first report to explore their cosmeceutical potential. Six antioxidants were detected in Sargassum sp., including fucoxanthin, (3S, 4R, 3'R)-4-Hydroxyalloxanthin, enzacamene N-stearoyl valine, 2-hydroxy-hexadecanoic acid, and metalloporphyrins. Meanwhile, three antioxidants detected in Kappahycus sp., namely Tanacetol A, 2-fluoro palmitic acid and idebenone metabolites. Three antioxidants are found in both algae species, namely, 3-tert-Butyl-5-methylcatechol, (-)-isoamijiol, and (6S)-dehydrovomifoliol. Anti-inflammatory metabolites such as 5(R)-HETE, protoverine, phytosphingosine, 4,5-Leukotriene-A4, and 5Z-octadecenoic acid were also found in both species. Sargassum sp. possesses higher antioxidant capacity as compared to Kappahycus sp. which may be linked to its number of antioxidant compounds found through LC-MS. Hence, our results conclude that Malaysian Sargassum sp. and Kappaphycus sp. are potential natural cosmeceutical ingredients as we aim to produce algae cosmeceutical products using native algae.