Microbes present in the digestive tract of an organism are of great importance. The microbial qualitative and quantitative composition represents the physical, physiological conditions, habits, habitats of the organisms as well as their association patterns. The microbes of digestive system have prominent role not only in the sustainability of the organism but also in the food processing industry. The marine cephalopods are one of the preferred marine food resources, next to marine fisheries. The current study aims to understand the microbial content in the digestive system of consumable cephalopods such as sepia and cuttlefish. The commercially available squids from the market and cuttlefish samples from fishing area were collected and used for this study. The organisms were dissected in aseptic conditions and bacteria collected from the guts of these animals. Culturable bacteria were isolated and, identified using gram characteristics as well as 16s r RNA techniques based molecular identification. The identified bacteria were reported to Gen Bank submission. Bacterial representation in the gut microbiome of cephalopods is low and showed distinct difference between cuttlefish and squid species. This low number of bacterial composition may be due to the habitat conditions or the association of bacteria with the animal requires further studies to understand. The commercial value of cephalopods as protein rich food prioritizes the need to address proper treatment process which can alleviate their presence in Indian food industry scenario. The inter and intra-species relation of microbes and metazoans and the associated macromolecules can be used for pharma industry also in future