The analysis of sequence variation in the mitochondrial and ribosomal regions has been shown to provide an efficient method for the identification of species in a wide range of animal taxa. In order to assess its effectiveness in the discrimination of genetic groups of Bemisia tabaci (Gennadius) species complex, populations from ten cotton cultivars were analyzed. MtCOI, and ITS1 sequences were evaluated to find out the genetic diversity through phylogenetic methods, viz., maximum likelihood and network neighbor-net analysis. Analysis of mtCOI-1 or barcoding region did not reveal significant variation. On the contrary, the mtCOI-II region revealed the presence of three B. tabaci genetic groups or subgroups corresponded with the global data. However, the ITS1 region could not discriminate these groups of the species complex. Our results indicate that more than the barcoding and ITS1 regions, mtCOI-II region or 3′ end of the gene will be more appropriate for the identification of variations among the populations of B. tabaci species complex.