Aquaculture is the major aquatic animal production segment. Problems like inbreeding depression, genetic drift, introgressive hybridization, etc. have been influencing the production of quality seeds negatively. Cryopreservation serves as a way-out for these problems and a possible answer to produce quality seeds and genetically improved varieties. It has been considered as a major strategy for conservation of fish genetic resources. Cryopreservation of fish gametes has been in vogue since 1953 and the technology is well studied and validated for many species. So far the milt of 200 fish species has been cryopreserved successfully. In this chapter, the importance of aquaculture in overcoming malnutrition, genetic issues affecting quality seed production, cryopreservation protocol employed for various fish species, problems faced in cryopreserving fish eggs and embryos and future of cryopreservation in aquaculture have been discussed.