This book helps us to understand the importance of the microbiome associated with finfish and shellfish inhabiting different locations and varied environmental and biological situations. It covers modern molecular tools for identifying microbiome composition and their precise identification at the species level. The book also covers the molecular structural composition of individual microbes, metabolite resources from microbiome species, their functional properties, and production aspects. Notable, the book covers the microbiome applications in the gut systems of finfish and shellfish to the digestion, nutrition, growth, reproduction, immune system, and vulnerability of the host to diseases. It also reviews diversity and functional properties, relationships with diseases, health status, data on species-specific metagenomics, and probiotic research. It highlights the relevance of microbial communities for the development of new and innovative bio-products to build bio and pharmaceutical industries, including aquaculture. This book is an invaluable source for researchers and professionals involved in fishery science, fisheries and aquaculture, fish biotechnology, and fish microbiology and pathology