Arthrospira is one genus of cyanoprokaryota for which information on toxin production exists for only a few strains. The purpose of this study was to investigate whether strains of Arthrospira fusiformis produce intracellular toxic compounds such as microcystins and anatoxin-a. The study was based on three strains of Arthrospira, two strains isolated from wastewater ponds in Mozambique and one from Lake Nakuru, Kenya. These strains were cultivated experimentally in different light intensities and salinities. Microcystins were analysed by ELISA and HPLC and anatoxin-a by HPLC. Toxicity analysis of the three strains, following the growth cycle, detected neither microcystins nor anatoxin-a. The results indicated that the strains selected were not toxigenic under the experimental conditions applied. Thus, the strains of A. fusiformis tested in the present study could be considered candidates for use in different applications such as in food supplements and in aquaculture.