The G protein-coupled receptor(gpcr)Tas2r38 is a bitter taste receptor that can respond to bitter compounds such as phenylthiocarbamide(PTC) and 6-n-PROPylthiouracil(PROP).This receptor was chosen because of its haplotypes (based on three residue site polymorphism) htas2r38pav, htas2r38avi are known to have a dramatically different response to ligands PTC and PROP. A docking study is performed to propose the best affinity between ligands PTC & PROP against the various active site of tas2r38 protein. The 3D structure of tas2r38 bitter taste receptor was predicted using GPCR-I-TASSER. The interaction of tas2r38 protein with ligands PTC & PROP were studied, their chemical structures were drawn using Marvin sketch and the potential ligands were optimized using pyrx. Meta pocket tool was used to predict the binding sites for htas2r38pav, htas2r38avi bound to Ptc & PROP respectively. Further, the docking studies of tas2r38 protein with Ptc & PROP was performed using pyrx tools and their interaction with the tas2r38 protein was visualized using discovery studio. The ligand PTC & PROP was docked on the protein PAV at the active sites 108,112,199 & 266 which showed a docking efficiencies of -4.6,-4.5,-4.7 &-5.3 respectively. Also, these ligands were docked on another haplotype AVI at the active sites 198,262,266 which showed a docking efficiencies of -4.7,-5.1, respectively. On the basis of their binding scores, it was predicted that the ligand PTC has a higher binding affinity to the haplotypes PAV and AVI as compared to the ligand PROP.