Phylogenetic analysis of the Bemisia tabaci (Gennadius) mitochondrial cytochrome oxidase I (mtCOI) sequence grouped populations into one of four major phylogeographic lineages, represented as groups from The Americas-Caribbean Basin (New World) (n = 41), Mediterranean-North Africa-Middle East (n = 47), Asia-Australia (n = 52), and Sub-Saharan Africa (n = 29). The mean genetic variation and percentage nucleotide identities indicated that whitefly populations from the Southeast Asian/Australian region were the most genetically divergent (1% per lineage/10⁶ yr), whereas the Western Hemisphere (Americas-Caribbean region) populations exhibited the lowest degrees of divergence. The phylogenetic tree for the genus Begomovirus (Geminviridae) coat protein (CP) revealed two major phylogeographic lineages with a basis either in the Eastern or Western Hemisphere, respectively. Within the Eastern Hemisphere lineage, the viral CP grouped in one of the three major geographical regions, which were analogous to the mtCOI for the respective geographically associated whitefly populations. Analysis of the CP for the Western Hemisphere viruses revealed two sublineages representative of the 1) North and Central Americas/Caribbean Basin, and 2) South American continent, respectively, which also were phylogeographically concordant with the two major Western Hemisphere B. tabaci mtCOI groups. Analysis of the base substitution rates and synonymous and nonsynonymous changes for the B. tabaci mtCOI coding region suggested that this gene has evolved under positive selection. In total, 26 polymorphic sites (11%) were identified for the species complex, and the fixation of certain amino acids was more evident within certain lineages or populations than others. Collectively, the majority of the 26 polymorphic sites were located at the C-terminal end of the mtCOI fragment that was examined herein. Of the 26 polymorphic sites, only two were net charge-altering amino acids (Y407H and G486K). The genetic differentiation coefficient (G_ST) for the B. tabaci complex was 59.9%, suggesting that at least moderate genetic differentiation has occurred for the four major extant phylogeographic lineages. This observation is in line with available extant biotic (exclusive vector of begomoviruses; transmission determinants linked to viral CP), morphological (no unique characters), and genetic evidence (single group based on mtCOI, 16SrDNA, and ITS-1 analysis), which supports the hypothesis that B. tabaci comprises a single albeit, cryptic species. Taxonomically, B. tabaci is a species complex, which likely has and continues to experience restricted gene flow in part as the result of geographical and/or host range restrictions.