Aphanothece halophytica is an extremely saline cyanobacterium. This study investigates the toxic nature of the organism and presents the first report of hepatotoxic cyclic heptapeptide microcystin analogs. The activity of the crude extract was investigated in mice. Results showed acute toxicity with mice death at about 4 h. Histopathological examination indicated massive alveolar hemorrhage and extensive congestion in liver cells. Increases in the levels of serum enzymes, i.e., AST (aspartate aminotransferase), ALT (alanine aminotransferase) and LDH (lactate dehydrogenase), provide further evidence of cell injury. An ELISA-based immunological detection kit confirmed the presence of microcystin analogs.