The Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a pest of agricultural and horticultural crops. The B. tabaci species complex consists of 36 morphologically indistinguishable putative species. This study evaluates the morphometric variations of developmental stages, puparia, and adults in three putative species of B. tabaci occurring in India. The genetic identity of these studied populations were confirmed by mtCO1 analysis and revealed that the population from Amravati, Ludhiana, and Delhi were clustered with Asia I, Asia II1, and Asia II7 putative species, respectively. The morphological comparisons showed that fourth instar and adult of Asia-II1 was comparatively larger than Asia-I and Asia-II7. The positioning of sensorial cone on antennal segment 7 is much apart, and away from the sensorium in Asia-II1 while these are comparatively adjacent in Asia-I and Asia-II7 for both the sexes. The multivariate statistical analyses reveal that 31 measurements in puparia, 23 of male and 22 of female show significant variations (P ≤ 0.01). This was supported by scatter graphs derived from principal components and canonical discriminant analysis (CDA), and separate clustering was obtained for Asia-I, Asia-II1, and Asia-II7. Overall 91 and 99% of the classifications were correctly attributed by CDA for puparia and adults which confirmed the distinction of these groups. The characters brought out in this study could be used as a population/putative species specific markers in B. tabaci species complex and these variations might enable distinguishing the other genetic groups too.