Five different isolates of Pakistani cannabis belonging to varying locations were analyzed for the presence of a reported tetrahydrocannabinolic acid (THCA) synthase marker or gene. The amplification of the marker (12 kb) from the five isolates confirmed them to be drug-type since the association of the marker with drug-type cannabis plants had already been established in other reports. The sequence analysis of the THCA synthase marker revealed two single nucleotide polymorphisms (SNPs) (i.e. A851→T851 and A883→C883) specific to Pakistani drug-type cannabis. Furthermore, the predicted protein sequence of the isolated sequences also showed two amino acid substitutions (D284→V284 and T295→P295) corresponding to the identified SNPs. However, the homology based three dimensional models of the inferred proteins generated via Swiss-Model-an automated online server did not project any changes at the active sites of the enzyme (THCA) due to D→V and T→P substitutions. The two missense mutations uncovered as a result of this study may assist in distinguishing the products of Pakistani cannabis among the smuggled materials.