This study presents simultaneous colorimetric detection of two very similar amino thiols viz. cysteine and homocysteine at their micro and sub-micromolar levels, respectively, through the aggregation of citrate capped silver nanoparticles. A rare kind of categorical naked-eye detection of homocysteine over cysteine was accomplished through the conjugation of these AgNPs with thiosulphate. The UV-Vis and SERS characteristics of these AgNPs were also more prominent with homocysteine compared to cysteine. The quantification of cysteine was performed in a pharmaceutic sample with an accuracy of 89 ± 5%.