Spirulina has emerged as the next-generation dietary supplement owing to its health benefits. Despite the advantages, there have been reports of contamination by cyanotoxins such as microcystins that can adversely affect human health. Hence, there is a need to develop a robust, efficient, and cost-effective method to detect microcystin-producing cyanobacteria in these food supplements. In this study, we have demonstrated a multiplex polymerase chain reaction (PCR) method for identification of microcystin-contamination in spirulina dietary supplements. This method involves simultaneous amplification of phycocyanin and microcystin B encoding genes ( pcb, mcyB). The sensitivity of the multiplex PCR was assessed, and the limit of detecting mcyB along with pcb was found to be 250 fg/µL. The presence of microcystin was detected in five out of seven fish food supplements indicating poor culture conditions. Hence, rigorous quality control is required for monitoring the spirulina food supplements.