This report describes in detail steps and considerations in the design of hatchery-based breeding trials for small indigenous fish species (SIS) native to South Asia. The aim of the trials is to develop to replicable protocols for the mass production of several micronutrient rich SIS. Once established and documented, techniques for mass production of SIS seed will be disseminated widely to hatcheries in the region to support the commercialization and scaling up of nutrition sensitive SIS aquaculture. The report provides detailed coverage of a wide range of important topics, including hatchery selection, water supply, pond layout and management, hatchery and incubator design, water quality requirements, predator management, induced breeding techniques, feeding, nursing, and transportation. The report also includes annexes covering topics such as protocols for setting up feeding experiments and experimental design, forms for daily record keeping, fish sampling, and water quality management, incubator design specifications, and a fish transportation checklist. As such, the report will serve as an invaluable resource to anyone interested in establishing fish breeding experiments for new species or involved in the management or operation of a freshwater fish hatchery.