A total of 13 species of microalgae and 14 strains of cyanobacteria, collected directly in the Portuguese coast and lagoons, were characterized for their fatty acid contents, focusing on two with a market potential — i.e. eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA); and another already with alternative (yet somehow more expensive) natural sources — i.e. α-linolenic (ALA) acid. The purpose of this work was their eventual inclusion as additives in food or feed. ALA was the most abundant PUFA in Nannochloropsis sp. (0.616±0.081mg FA .L culture −1 .d −1 ), and EPA in Phaeodactylum tricornutum (0.148±0.013mg FA .L culture −1 .d −1 ); Pavlova lutheri was particularly rich in EPA (0.290±0.005mg FA .L culture −1 .d −1 ) and DHA (0.140±0.037mg FA .L culture −1 .d −1 ). Despite several previous reports on similar topics and encompassing some of our microalgal species, the wild nature of our strains accounts for the novelty of this work — in addition to the characterization of a few wild cyanobacteria. Eustigmatophyceae class was the best producer of ALA, while Prymnesiophyceae was the best for EPA and ALA. Nodularia harveyana exhibited the highest ALA level (0.611±0.022mg FA .L culture −1 .d −1 ) and Gloeothece sp. was highest in EPA (0.030±0.004mg FA .L culture −1 .d −1 ).