Caspian trout (Salmo trutta caspius Kessler, 1877) is an endemic migratory subspecies in the Caspian Sea, possessing ecologic-economic and biodiversity greatly value. Among habitat factors, temperature and its possible effects on the Caspian trout genome were considered in this research. During Embryonic developmental stages (fertilization–hatching), genomic alterations of single cells were assessed by Comet assay technique in three thermal treatments (4, 8, 12oC). After artificial propagation of wild broodstocks, the batches of eggs (No. 500), were transferred to well equipped incubators with constant temperatures, water recycling systems by REDD(spawning area of trout)water, 3 stages water filtration (Si+Active Coal+Zeolite), UV-C application on effluent of each incubator and DO – pH – temperature digital controllers in 3 replicates. 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 technique were applied on samples for evaluation of Comet Tail length (TL), DNA in tail (DT) and Tail Moment (TM) indexes (CometScore software ©2013 TriTek Corp) as DNA damage markers. Significant difference between thermal treatments (P<0.05) and 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 mean values measured as 18.07±6.3, 9.72±1.9 and 31.47±2.8 and then TM mean values measured as 15.27± 4.1, 1.21±0.2 and 95.25±8.6 for 4, 8, and 12°C treatments respectively. Warm (12°C) treatments demonstrated greater DNA damages in comparison to the others. TM explained better information in comparison with TL & DT in all analyzed samples. In conclusion, temperatures out of optimal thermal conditions could significantly affect Caspian trout genome which could be subject of management considerations pertaining to Caspian trout stocks rehabilitation and captive rearing strategies.