TNT is one of the most commonly used nitro aromatic explosives used for landmine and military purpose. Due to the significant detrimental effects, contamination of soil and groundwater with TNT is the major concern. Driven by the need to detect trace amounts of TNT from environmental samples, this article demonstrates for the first time a highly selective and ultra sensitive, cysteine modified gold nanoparticle based label-free surface enhanced Raman spectroscopy (SERS) probe, for TNT recognition in 2 pico molar (pM) level in aqueous solution. Due to the formation of Meisenheimer complex between TNT and cysteine, gold nanoparticles undergo aggregation in the presence of TNT via electrostatic interaction between Meisenheimer complex bound gold nanoparticle and cysteine modified gold nanoparticle. As a result, it formed several hot spots and provided a significant enhancement of the Raman signal intensity by 9 orders of magnitude through electromagnetic field enhancements. A detailed mechanism for termendous SERS intensity change has been discussed. Our experimental results show that TNT can be detected quickly and accurately without any dye tagging in lower pM level with excellent discrimination against other nitro compounds and heavy metals.