Caspian trout (Salmo trutta caspius Kessler, 1877) as endemic migratory fish, possessing great ecological economic and biodiversity value. Among the habitat drivers, temperature related effects on the genome were considered in this research. During the embryonic developmental stages, genomic alterations of single cells were assessed by Comet assay. After artificial propagation of wild broodstocks, the batches of eggs, were transferred to incubators with constant temperatures, REDD water recycling, 3 stages water filtration, UV-C application on effluent of each incubator and DO–pH–temperature control. Samples were collected from normal (8°C), cold (4°C) and warm (12°C) treatments on eyed egg, alevin and larval stages. Single Cell Gel Electrophoresis were applied on samples for evaluation of Comet Tail length (TL), DNA in tail (DT) and Tail Moment (TM) indices as DNA damage markers. Comparison between mean values of Comet TL index indicated 85.19 ±9.2, 9.88 ±2.3 and 256.54±14.6 for 4, 8 and 12°C treatments, respectively. DT were 18.07±6.3, 9.72±1.9 and 31.47±2.8 and then TM were measured as 15.27± 4.1, 1.21±0.2 and 95.25±8.6 for 4, 8, and 12°C treatments, respectively. Significant difference between thermal treatments (p〈0.05) observed. Warm treatments demonstrated greater DNA damage in compare with others. TM explained better information in comparison with TL and DT in all analyzed samples. In conclusion, temperatures out of the range of the optimal conditions could significantly affect Caspian trout genome which could be the subject of management considerations pertaining to Caspian trout stocks rehabilitation and captive rearing strategies.