The whitefly Bemisia tabaci (Gennadius, 1889) (Hemiptera: Aleyrodidae) is one of the most important pest species on cotton in the Cukurova Plain as well as in all cotton growing areas of Turkey. Although numerous studies on population dynamics, population development and parasitism were conducted on B. tabaci in the Cukurova Plain, there has been a few studies on the species complex of B. tabaci for this region. The aims of this study were to present genetic polymorphism and species composition of B. tabaci collected from cotton fields of Cukurova Plain of Turkey between 2006 and 2011 (except 2010). Polymerase chain reaction (PCR) products were generated from a mitochondrial gene, cytochrome oxidase I (COI), and a nuclear gene region (ITS1). PCR products were purified and sequenced. Maximum likelihood (ML) and Bayesian analyses were used to estimate trees. Restriction fragment length polymorphism (RFLP) method was also applied to support results of sequence analysis and differentiating the MED and MEAM1 species of B. tabaci populations. From 51 sequences 38 of them were determined as B. tabaci MED species, and 13 of them were B. tabaci MEAM1. All samples collected in 2006 were placed in the B. tabaci MEAM1 clade with some samples collected in 2011. All PCR products were studied by RFLP method and we were able to differentiate MED and MEAM1 species of B. tabaci. MED species was determined as dominant on cotton in Cukurova Plain of Turkey.