Abstract Fish deformities are detrimental to aquaculture and conservation initiatives; it is also an ethical problem and causes substantial financial losses to the aquaculture industry. The exact mechanism of deformities is still a mystery. Several factors cause deformities in fish; it seems that the deformations are inevitable but can be minimised by adopting good aquaculture practices such as proper broodstock husbandry, standard breeding and larval rearing protocol, management of water quality parameters, and providing nutritionally balanced feed, especially to the broodstock and developing larvae. In addition, it can be minimised by early detection of deformities, especially at the embryonic and larval stages. Monitoring of stocking materials should be an essential part of responsible aquaculture and conservation programmes; stocking materials should be free from any types of deformities as it affects not only aquaculture production, profitability and success of conservation programmes but also the reoccurrence of deformities in nature. The mechanism behind deformities and the development of low‐cost, robust methods/tools for detecting deformities in fish remain a challenge. Still, the opportunity exists to develop a robust marker that can predict deformities even at early embryonic and larval stages.