Algal mass productions are widespread events throughout the world. Most research deals with the environmental impact, ecology and toxicity of these phenomena, but the algae are also promising sources of bioactive natural products, and also are potential food additives. In the current study, we aimed to characterize the carotenoid composition of three non-toxic algal isolates with distinct taxonomical position, namely Dunaliella salina, Euglena sanguinea and a Nostoc strain. The strains were screened for carotenoid composition with HPLC–UV–APCI-MS with comparison with authentic standards. Carotenoids were purified with open column chromatography, and characterized by LC–UV–MS and NMR. All three species contained a high amount of carotenoids. The composition of the carotenoid pattern was somewhat different compared to literature data. The Dunaliella carotenoid fraction contained lutein (52.1% of total carotenoid), β-carotene (13.1%), violaxanthin (11.5%) and neoxanthin (6.2%) as chief compounds. The chief carotenoids in the Nostoc strain was echinenone (34.9%), while the main components of the Euglena isolate were diatoxanthin (39.0%), lutein (23.7%), an unidentified carotenoid (9.6%) and β-carotene (5.4%). Diatoxanthin is identified by NMR spectroscopy. The carotenoid patterns of the examined strains are somewhat different from the patterns described in the literature. This can be the results of genetic or environmental differences, or combinations thereof. Despite these differences, our study shows the potency of these algae in production of carotenoids, and possibly, usage as food additives. •Characterization of the carotenoids of a lutein-rich Dunaliella salina strain•Characterization of the carotenoids of an echinenone-rich Nostoc strain•Characterization of the carotenoids of a diatoxanthin-rich Euglena sanguinea strain•Three non-toxic algae were shown to be excellent natural sources of carotenoids.