The association between Bemisia tabaci mitotypes and cotton leaf curl outbreaks in Pakistan was investigated using the mitochondria cytochrome oxidase I gene (COI) as a molecular marker. The 3′-651 base fragment has been used to resolve B. tabaci phylogenies. However, the 5′-618 base fragment was nearly unexplored. Phylogenetic analysis for 829 whiteflies from 11 districts in two provinces of Pakistan, indicated all haplotypes grouped on the Asia II major clade, with Asia II-1 mitotype predominating, at 84%, compared to Asia II-5 and II-7, at ∼16%, combined. The 3′- and 5′-fragment tree topologies were similar, while the concatenated topology was unique in some respects. Comparisons of segregating sites within the 3′- and 5′-loci, at third codon positions, 71 and 47, and of transitions to transversions (Ti/Tv) ratio of 2.93 and 5.9, respectively, showed the 3′-locus was most informative, while nucleotide diversity (π) was highest for the 5′-end, indicating both fragments contributed to concatenated tree structure. The extent of haplotype diversity, measured by Tajima's D, R², and Fu's F analyses, revealed significant demographic expansion for Asia II-1 and II-7 mitotypes. The bottleneck that preceded the expansions was evident in the temporal changes in mtCOI polymorphisms beginning in ∼1990s, a timeframe known to have coincided with the adoption of a high-yield whitefly-susceptible cultivar in 1988, followed by pesticide overuse. These two cooperating phenomena appear to have exerted selection on the cotton leaf curl disease (CLCuD)-whitefly complex, resulting in the emergence of a resistance-breaking begomovirus as the polyphagous Asia II-1 mitotype underwent a genetic expansion that led to ‘a perfect storm’.