| Cotton Leaf Curl Disease (CLCuD) being caused by begomoviruses exclusively transmitted by Bemisia tabaci cryptic species comprised of genetic variants which could be differentiated by mitochondrial cytochrome oxidase I (mtCOI-3 ʹ ) gene. Most numerous cryptic species is Asia II-1recorded all over in Pakistan whereas North Africa-Middle East (NAFME) previously known to be found in the Sindh province but now also reported in the Punjab province. This study revealed that overall diversity of whitefly cryptic species in Pakistan is higher than previous studies. Some whitefly cryptic species cause direct damage to the crops by feeding and indirectly by transmission of plant viruses that reduce the crop yield and quality. Cotton leaf curl virus (CLCuV) management is difficult due to multiple virulent strains and higher recombination rate that is a serious threat to the cotton crop of the last two decades in Pakistan. Alternate host plants belonged to vegetables, weeds, and mixed farming practices helped the evolution of new viral and whitefly species. The CLCuD develops resistant cultivars against CLCuV and screening of new host resistance forms. Applications of DNA markers to induce resistance into the cultivars and editing of genome are some of the good practices contributing to suppress this disease. The study is helpful in understanding population dynamics of whitefly cryptic species interaction with the begomoviruses and alternative host plants which is imperative to devise effective management strategies for CLCuD and its vector whitefly.