The whitefly Bemisia tabaci is a species complex including at least 24 morphologically indistinguishable species among which the Mediterranean (Med) and Middle East-Asia Minor I (MEAMI) species containing the biotypes commonly known as Q and B, respectively. These B and Q biotypes (hereafter referred to as MEAMI and Med species) are the most invasive agricultural pests of the B. tabaci complex worldwide. The spread of MEAMI and more recently of Med species into regions already invaded by other B. tabaci populations has been frequently seen to lead to their displacement by Med species. In Tunisia, in contrast to usual observations in the Mediterranean basin, Med and MEAMI species have been seen to co-occur in the main crop producing regions. Based on fine population genetics and field spatial distribution analyses, we found that the co-existence of these two interacting species was based on habitat partitioning including spatial and hostplant partitioning. Although they co-occurred at larger spatial scales, they excluded one another at sample scale. We observed neither spatial overlapping nor hybridization between MEAMI and Med B. tabaci. Vegetable crops were the main hosts for MEAMI specimens while 99.1% of the B. tabaci collected on the ornamental, Lantana camara, were Med specimens. Different patterns of genetic diversity were observed between the two species, as well as among Med specimens sampled on the ornamental versus vegetables, with the highest genetic diversity found in Med B. tabaci sampled on L. camara. These findings lead us to focus our discussion on the role played by lantana, human pressure, and competition, in the spatial and genetic patterns observed in the whitefly B. tabaci.