Objectives: This present study aims to understand the landscape structures as well as the environmental (climatic) factors influencing the genetic diversity of fly populations in the agroecological area of Niayes. Methodology and results: Landscape composition of different mango orchards of different typologies were determined after drone mapping and fly samples carried out on Kent mangoes. The molecular biology process carried out on about fifty individuals made it possible to obtain sequences of the Cytochrome oxidase I. The results revealed a high genetic diversity and structuring in the populations of flies dependent on single-variety orchards and in contrast a very low diversity in diversified orchards. The genetic diversity appears closely linked to the landscape composition of orchards. Orchards with the most diverse landscapes have populations of B. dorsalis with lower diversity and genetic structure. Conclusions and application of findings: The results made it possible to objectively understand the diversity of the landscape associated with the different mango production systems in relation to the genetic variability of the populations of B. dorsalis in the Niayes area. Genetic analyses revealed a low level of polymorphism, diversity and genetic structuring of the fly population subservient to the diversified orchard of Carmel and a greater diversity and polymorphism in the population of Notto (monovarietal orchard). A strong negative correlation is noted between the landscape diversity and the genetic diversity of the populations of B. dorsalis underpinning a maintenance of the populations at the level of the orchards diversified in low numbers from one mango production season to another and seasonal appearances in single-variety industrial orchards with populations from elsewhere. This study provides new elements which, if confirmed by larger-scale studies, would make it possible to refine the fly control techniques currently applied.