The protist Euglena gracilis has unique and varied metabolic pathways and is an excellent source of dietary protein, essential amino acids, lipids, β-1,3-glucan paramylon, and vitamins. A key concern about using E. gracilis to generate feed and food ingredient products is the possibility that it makes marine toxins. The current investigation therefore used comprehensive analyses of known marine toxin biosynthesis pathways and key genes to evaluate the E. gracilis strain Z for its ability to produce any marine toxins under various fermentation conditions. The major results of this investigation reveals that: 1) E. gracilis does not have the genes essential for the biosynthesis of microcystin, cylindrospermopsin, saxitoxin, brevetoxin, complex toxic polyketides, or domoic acid; 2) E. gracilis does not express an essential gene for the biosynthesis of okadaic acid under heterotrophic fermentation conditions; 3) Phylogenetic analysis using 18S rDNA sequences concluded that E. gracilis is not grouped with any known euglenophycin-producing Euglena species. This study provides a thorough investigation and reviews marine toxins and their genetic mechanisms and metabolic pathways; thus, it can serve as supporting documentation for any feed or food ingredients derived from Euglena gracilis.