The purpose of this study was to analyse the influence of water salinity on fry development of hybrid Malaysian mahseer under controlled conditions. The physical changes and the tolerance limits in stress condition due to salinity exposure were determined in a recent study. The experiment was conducted in the wet laboratory, Department of Aquaculture. Ovatide hormone (0.4 ml/kg) was used to induce ovulation of female Barbonymus gonionotus, while the sperms were collected from the male mahseer. The recent study was done to investigate the effects of salinity on hybrid fish in terms of survival, growth, histological changes, blood content and hepatosomatic index (HSI) under laboratory conditions. This study exposed the fish to different concentrations of salinity (0, 3, 6 and 9 ppt) for 3 months. All treatments were in triplicate, labelled and arranged in a randomized design. Fry were fed until satiation twice a day and 30% of water was changed daily. The highest growth rate and survival rate (84%±7.78%) of fry were obtained in 3 ppt water salinity, while the lowest growth performance and survival rate (67%±13.45%) occurred at 0 ppt. The highest body gains and lengths of fry were observed in 9 ppt water salinity. However, significant histological alterations were observed in 9 ppt water salinity which caused major anomalies such as structural alterations in portal vein, vacuolation, necrotic hepatocytes, aggregation of blood cells and melanomacrophages. New strains of hybrid Malaysian mahseer were successfully bred. Optimal condition for fry Malaysian mahseer hybrid was 3 ppt water salinity. The results show that excessive salinity in the aquatic conditions affected negatively the health of the hybrid fish.