Trichoderma isolates were collected from varied agro-climatic zones of India and screened for high temperature and salinity tolerance. Among all the isolates tested, T. asperellum, TaDOR673 was highly tolerant to heat shock of 52°C with a mean spore count (log c.f.u/ml) of 4.33. The isolate after recovery from heat shock possessed higher germination rate and biomass production compared to its wild counterpart, upon prolonged exposure to 37°C. Under stress, TaDOR673 accumulated >15% of trehalose and >5% of mannose and raffinose compared to the wild type strain signifying their role in stress tolerance. T. asperellum, TaDOR693 and T. asperellum, TaDORS3 were identified as superior salt-tolerant isolates. Interestingly, TaDOR673 also possessed similar tolerance levels to increasing saline concentrations as indicated by its improved colony growth under stress conditions. T. asperellum, TaDOR673 and T. asperellum, TaDOR7316 effectively controlled the collar rot disease in groundnut by 79.7% when screened in vitro and in vivo. Thus, the study identified a potential thermotolerant and saline tolerant strain of Trichoderma, TaDOR673 that could be used as potential bioagent in stressed soils.