Among the new entries in the food supplements sector, an important place must be assigned to nutraceuticals containing microalgae, nowadays accounting for a large and rapidly expanding market. The marketed products are mainly based on three production strains, i.e., Spirulina and Chlorella, followed at a distance by Klamath. It is a composite situation, since two of them are cyanobacteria and the second one is eukaryotic. The reality is that each presents similarities in shape and appearance concerning the marketed form and several utilizations, and peculiarities that need special attention and adequate studies. First, general information is reported about the current scientific knowledge on each microalga, in particular the nutritional value and properties in prevention and wellbeing. Second, original studies are presented concerning the quality control of marketed products. Quality control is a key argument in nutraceuticals validation. Microalgae are particular organisms that need specific approaches to confirm identity and validate properties. The proposed control of quality is based on microscopic analysis of the morphologic characteristics. The final parts of this paper are dedicated to the need for specificity in uses and claims and to considerations about the future of microalgae in food supplements.