In the recent years stressful environment caused by climatic variables and resultant atmospheric and soil moisture deficit with high/low temperatures and high solar light intensity are observed to be limiting factors for the establishment of young rubber plants in the traditional and non-traditional rubber growing areas in India. In this context identification of specific functional and molecular markers are essential to screen vast number of available elite and pipeline clones, ortet selections and wild germplasm accessions of Hevea brasiliensis for stress tolerance. Relative abiotic stress tolerance potential of many clones and wild accessions were evaluated using key physiological parameters such as leaf water potential, chlorophyll content, Q PSII activity, photosynthetic oxygen evolution and CO2 assimilation (Pn) rates. A consistently over expressing chloroplast low molecular weight (23.8 kDa) protein was observed in drought and highlight tolerant clones. Further, this protein was validated as a physiological marker for drought tolerance potential of Hevea by relating stability of physiological parameters with its abundance under stress conditions. Similarly consistently over expressing stress proteins (60 and 17 kDa) were identified in mesophyll cells of cold stress tolerant clones. A few genes conferring tolerance to extreme environmental factors were identified. Significant up-regulation of NAC tf, LEA 5 and WRKY tf was noticed in drought tolerant rubber clones and wild accessions, while its expression level was relatively smaller in susceptible clones/accessions indicating strong association of these genes with stress tolerance and can be used as potential markers for screening clones suitable for marginal areas of rubber plantation.