The growing demands and high costs of commercial Artemia cysts and the establishment of new shrimp hatcheries and farms have caused people to search for local sources of Artemia, putting special attention on their nutritional characteristics. As an essential step to determine the biochemical composition of Artemia, the fatty acid profiles of decapsulated cysts from six tropical salterns of southern México [Campeche (1), Oaxaca (1), and Yucatán (4)], two of Cuba (Camagüey and Guantánamo), and from a temperate site (San Francisco Bay, USA) (SFB) were analysed using direct transesterification and gas chromatography-mass spectrometry. Of 51 fatty acids identified, C16:0 (hexadecanoic), C16:1 n5 (hexadecenoic), C18:1 n9 (octadecenoic), C18:1 n7 (octadecenoic), and C18:2 n6 (octadecadienoic) were the major compounds found. The SFB strain from a temperate area showed significant differences from the rest of the samples of tropical origin, having a greater concentration in the fatty acids 18:2 n5 (10, 13-octadecadienoic), 18:3 n3 (octadecatrienoic), and 18:4 n3 (6, 9, 12, 15-octadecatetraenoic). The SFB strain showed the lowest proportion of mono-unsaturated fatty acids. Based on the fatty acid composition, the Artemia strains studied can be assessed as “freshwater” type, except for the one from Oaxaca that had a “marine” type profile characterized by 3% to 4% of the fatty acid C20:5 n3 (eicosapentaenoic).