Bemisia tabaci Gennadius is a major pest on cotton and vegetable plants in Africa. It is considered as a cryptic species complex. Identification of the most damaging species such as the Middle East-Asia Minor 1 (B biotype) and Mediterranean (MED) (which contains the Q and Africa silverleaf (ASL) biotypes) species represents an important step towards the management of B. tabaci. Some data on the geographical distribution of the B. tabaci species complex exist in Burkina Faso, Benin and Togo, but data on the pest's invasion and displacement dynamics, in relation to time, are lacking. Here, molecular markers (mitochondrial cytochrome oxidase, mtCO1) were used to determine the identity of B. tabaci. Our results illustrate population dynamics on cotton and vegetable plants between 2007, 2009 and 2010. On cotton in southern Togo, ASL was predominant and found in sympatry with Q1. Its frequency decreased slightly over time, i.e. from 92% in 2009 to 90% in 2010. In Burkina Faso, Q1, Q3 and ASL biotypes showed different temporal and spatial distribution patterns. There, Q1 dominated on cotton plants throughout the study. This work provides relevant information about the population dynamics of B. tabaci MED species in two West African countries, Burkina Faso and Togo, in connection with pest management programmes.