Diseases are considered to be the major constraint in aquaculture production. They cause mortality in shrimp larviculture and fish hatcheries. They are also a constraint on consistent production of fish and shell fish. Traditionally, the control of diseases in aquaculture has relied on the use of chemical compounds. More recently probiotic microorganisms and vaccination or other forms of immunostimulation have also been employed. The abuse of antimicrobials can result in the development of resistant strains of bacteria. Such resistance can be readily transferred to other strains, either following alterations to the existing genome or by transfer of genetic material between cells through plasmids or bacteriophages. The massive use of antibiotics for the control of diseases has been questioned by acquisition of antibiotic resistance in disease causing agents and the need of alternative measures to control these diseases is of prime importance. In recent years, probiotics have a center stage and are used as alternative measures to control the fish diseases. Probiotics have been used by man for millennia since the time humans first consumed fermented milk products. Probiotics can be essential for the normal digestive, endocrine and immunological functions of the bowel. They inhibit pathogenic microorganisms and have been used therapeutically to treat a variety of gastrointestinal and even systemic disorders. Probiotics transiently colonize the bowel and except when used to treat an acute disorder, must be regularly consumed to maintain benefit. Use of microbial probiotics to promote health maintenance and disease prevention and control is now widely accepted as the new ecofriendly alternative measures for sustainable aquaculture.