Abstract: Whitefly, Bemisia tabaci (Genn.) is an important sucking plant sap pest of field, horticultural and ornamental plants causing feeding injuries besides spreading plant diseases by acting as a vector of Gemini-viruses. The polyphagous nature of the pest makes it as a highly complex species. The influence of six host plants belonging to three different plant families utilized by the species on the population differences at molecular level was attempted using Random Amplified Polymorphic DNA (RAPD) markers. Fifteen RAPD primers were screened seven of them were produced 218 DNA fragments, 209 of them were polymorphic while the other nine bands could be considered as common for B. tabaci. Total number of bands obtained from each primer ranged from 23-44 with an average of 36.33 bands per primer. RAPD-PCR analysis led to identification of 42 polymorphic markers holding specificity for these hosts' populations. Phylogenetic relationships among the studied populations using this technique clearly separated these six populations into two main clusters with similarity matrix percentage of 88 and 64%. These results indicated that B. tabaci may have different genotypes on adaptations to certain host plant species in Egypt.