Mitigating climate change and global warming through carbon sequestration of tree ecosystem is of prime importance due to cost effective, environment friendly and ecological sustainability. Urbanization is a part of development and generally rubber plantations were usually removed for this purpose especially in Kerala, the southern state of India. Besides commercially high yield of latex, the economic produce of rubber plant and the associated income, rubber tree is fairly good sink for carbon in its biomass with an average carbon content of 42 per cent and substantial carbon stock in soil. This study pointed out the serious carbon sink loss from the removal of rubber plantation for urbanization, one of the major development activities which resulted in the damage of the self-sustained carbon friendly and economically sound perennial rubber ecosystem. The present popular clone (RRII 105) existing in major share (85 %) of the total rubber cultivation in India accounts carbon sink loss 57t/ha, 57.5t/ha, 43.2t/ha for 23 years and 148t/ha, 75t/ha and 62.1t/ha for 30 years from biomass, litter fall and sheet rubber respectively. The establishing modern clones RRII 414, RRII 429 and RRII 417 having higher growth rate and biomass recorded still higher (44–50 per cent) carbon sink loss compared to the existing popular clone RRII 105. The carbon sink loss in the form of stored carbon in soil is 56.5 with soil carbon content between 1.2 to 2 per cent. Due to the growth variation in extreme climatic conditions, the clones recorded differences in carbon stock and thereby carbon sink loss. The central region of Kerala showed higher loss and lower loss was in the drought affected northern region than South region. The total carbon sink loss for 23, 30 years were 214.2 and 341.5 t/ha respectively. Maintenance of green spaces/areas including vegetation having higher C-sequestration potential and trees having higher lignin content to increase carbon capture for mitigating the impact of removal of plantations especially in high altitude to some extent in the scenario of inevitable developmental activities and urban developments to become environment friendly. From the study it was clear that the removal of rubber plantation affecting the carbon sink loss greatly and thereby the CO2 mitigating capacity and is a serious matter of concern.