Flying fishes are ocean living surface fish that leap out of the water and glide long distances using elongated pectoral fins and wing gliders. While swimming on the surface or close to it, the pectoral fins are held close to the body. The flying fish fishery is an important seasonal fishery on the east coast of India extending from Chennai to Point Calimere along the Coromandel Coast.There is a scarcity of reference that gives a complete account of the proximate composition and heavy metal concentration and pathogenic microbes of flying fishes. Hence a comparative study of proximate composition, heavy metal concentration and pathogenic microbes of two species of flying fishes, Cypselurus spilopterus and Hirundichthys coromandelensis was undertaken. The proximate composition analysis of the fishes helps to know the nutritional value. Analyzing the heavy metal concentration helps to identify the quality of the fishes, whether it contains all the microelements in optimum level.