The cotton whitefly (Bemisia tabaci Genn.) is a major pest of cultivated plants in tropical and subtropical regions. In this study, the genetic diversity between populations and various biotypes of B. tabaci collected from Hatay, Adana, Icel, Antalya, Mugla, Aydin and Denizli provinces of Turkey were investigated using mitochondrial cytochrome oxidase subunit 1 (mtCOI) sequences. Thirty-two nucleotide variations were found in a 617 bp mtCOI sequence of the among the populations studied. Phylogenetic analysis divided the B. tabaci populations of Turkey into two groups clustering around the main Middle East-Asia Minor 1(MEAM1) and Mediterranean (MED) groups, (i.e. the so-called B and Q biotypes respectively). Mediterranean species were also divided into two subgroups. The populations from Aydin and Denizli provinces identified as the Qw haplotype were closely related to populations of Greece, whereas the remaining samples were identified as the Qe haplotype. This study indicated that the biotype status of the B. tabaci populations might have changed from year to year depending on several factors, such as insecticide resistance, host plant preferences, and climate niches to understand the factors causing changes in the biotype structure, pest populations should be monitored, and surveys must be conducted at regular intervals.