Possibility exists that qPCR primers could bind to different variants of template in the sample, thereby, leading to the amplifications of different variants and generations of amplicons slightly differentiated in sequence. Melt curve analysis has been proposed to be capable of differentiating the amplicon variants due to their unique melting temperature. This work uses theoretical modelling to put this idea to the test on different Helicobacter species and different Helicobacter pylori isolates. Results from an in-house MATLAB melting temperature calculation tool suggests that melting temperature of 16S rRNA gene of different Helicobacter species and different H. pylori isolates are clustered around 86 oC within a fractional degree. This means that the 16S rRNA amplicons of different Helicobacter species and different H. pylori isolates are unlikely to be differentiated by PCR melt curve analysis. Overall, the results suggests that 16S rRNA gene of different Helicobacter species and different H. pylori isolates are closely related in sequence, and therefore could not be differentiated by melt curve analysis.