Exposure to extreme environmental heat or cold during military activities can impose severe thermal strain, leading to impairments in task performance and increasing the risk of exertional heat (including heat stroke) and cold injuries that can be life-threatening. Substantial individual variability in physiological tolerance to thermal stress necessitates an individualized approach to mitigate the deleterious effects of thermal stress, such as physiological monitoring of individual thermal strain. During heat exposure, measurements of deep-body (Tc) and skin temperatures and heart rate can provide some indication of thermal strain. Combining these physiological variables with biomechanical markers of gait (in)stability may provide further insight on central nervous system dysfunction - the key criterion of exertional heat stroke (EHS). Thermal strain in cold environments can be monitored with skin temperature (peripheral and proximal), shivering thermogenesis and Tc. Non-invasive methods for real-time estimation of Tc have been developed and some appear to be promising but require further validation. Decision-support tools provide useful information for planning activities and biomarkers can be used to improve their predictions, thus maximizing safety and performance during hot- and cold-weather operations. With better understanding on the etiology and pathophysiology of EHS, the microbiome and markers of the inflammatory responses have been identified as novel biomarkers of heat intolerance. This review aims to (i) discuss selected physiological and biomechanical markers of heat or cold strain, (ii) how biomarkers may be used to ensure operational readiness in hot and cold environments, and (iii) present novel molecular biomarkers (e.g., microbiome, inflammatory cytokines) for preventing EHS.