The recognition and use of algae in the very trend-driven cosmetic industry is progressively increasing. Up to now, the main focus was on large seaweeds and a limited number of microalgae. However, motile microalgae, flagellates, remain underscored in this aspect, although some of them are utilized commercially. Flagellates from different taxonomic groups occupy various habitats and contain bioactive high-value multifunctional compounds, some of which are novel. Moreover, they may simultaneously produce different substances, which together with the development of downstream processing technologies, makes them a promising source for modern biotechnology. The present review covers data on 411 strains, 251 species from 110 genera from 6 phyla, and is oriented generally towards less explored flagellates. It demonstrates their great potential as bearers of interesting novel compounds that can be beneficially applied in modern cosmetics. Safety aspects of both sources and products are also discussed. Considering the gaps in the knowledge, the necessity to expand the research on both well-known and yet unexplored microalgae is shown, encouraging the development of upstreaming processes, including phycoprospecting. Last but not least, this paper outlines the role of living culture collections and of using good taxonomic expertise before running the biochemical tests, cultivation, and bioengineering experiments.