Sphingolipids are not only essential components of biological membranes but also play numerous other vital functions in living cells. Moreover, they are major constituents of the outermost layer of human epidermis which acts as permeability barrier of the skin. Therefore, they have a high potential to be used in a wide variety of application fields such as antibacterial and antifungal agents, active pharmaceutical ingredients of therapeutics as well as active ingredients in cosmeceutical or nutraceutical formulations. However, their chemical synthesis is a complex and cost-intensive process. As the yeast Wickerhamomyces ciferrii has been found to be a natural producer of acetylated sphingoid bases, it provides a promising alternative for their biotechnological synthesis. In the last years, this yeast has been established by classical strain improvements as well as modern genetic engineering for the industrial production of phytosphingosine. Moreover, routes for the synthesis of sphinganine and sphingosine have been implemented. This mini-review summarizes the current knowledge about biosynthesis of sphingoid bases, genetic engineering of W. ciferrii for their biotechnological production, as well as their applications in cosmetic formulations.