In the present study, 180 Persian sturgeon fries at releasing weight with average weight of 1. 8 ± 0. 6 g were exposed to three different salinity levels including 0 (fresh water), 6 and 12 ppt in 96-hour and 10-day periods for measuring their gill metabolites by H-NMR based metabolomics. The results showed that changes in salinity caused changes in the metabolites involving in osmotic regulation, such as betaine, methionine, and threonine and also changes in energy metabolites such as alanine, DMA, and glutamine. After studying the metabolites, it was found that alanine, betaine, serine, glutamine, threonine, dimethylamine, fumaric acid, methionine, tyrosine, leucine, acetone, isoleucine, serine and formic acid showed significant differences between fresh and 12 ppt water. The metabolites including alanine, betaine, glutamine, threonine, dimethylamine, fumaric acid, methionine, acetic acid, and choline were significantly different between fresh and 6 ppt water, and the metabolites including lactic acid, formic acid, and serine showed significant differences between 6 and 12 ppt water (P<0. 05). The need to provide energy and immunity in conditions of increasing salinity caused significant increasing in branched amino acids, lactate and alanine in 12 ppt salinity water in compare to fresh water (P<0. 05). Methionine and taurine which are responsible for coping with salinity stress, as well as glutamine and fumaric acid, which change at oxygen stress, also significantly increased (P <0. 05) between fresh and 12 ppt salinity water. The betaine metabolite which acts as osmotic regulator in salinity conditions and prevents intracellular water loss, showed a significant reduction (P <0. 05) in 12 ppt water in compare to fresh water. The results of this study indicate that fumaric acid, methionine and branched chain amino acids are the most important biomarkers of salinity tolerance in Persian sturgeon fries.