In West Africa, the use of organophospates and pyrethroid insecticides to control cotton pests has led to the evolution of resistance in field populations of Bemisia tabaci Gennadius. Three pest management programs have been commonly recommended: the Conventional Program (CP) where 6 treatments are applied, the use of Bt cotton plants for which only 2 applications of neonicotinoids are required and that has been adopted in many countries, and a biological program (BP) without any chemical treatment. The present study aimed to determine the influence of these practices on the frequency of mutations that confer resistance to pyrethroids (mutation L925I in the para-type voltage-gated sodium channel gene) and organophosphates (mutation F331W in the acetylcholinesterase enzyme ace1: allele Ace1 R) in B. tabaci populations using Bt cotton and CP areas in Pô and Saria (Burkina Faso), CP and BP areas in Kandi (Benin) and only CP areas in Tové and Infa (Togo). All individuals sampled belonged to the MED (biotypes MED-Q1) and Africa Silver Leafing (ASL) species. MED-Q1 was found in sympatry with ASL in Burkina Faso both on CP and Bt cotton areas at variable frequencies. In Togo and Benin, only ASL was found, except in Tové where MED-Q1 was also detected, but at low frequency. Frequencies of mutations that confer resistance varied between localities and species but we did not find any strong evidence of a relationship between the pest management program and these frequencies except for the allele Ace1 R in Burkina Faso for which the frequencies decrease when chemical applications are reduced. This study provides valuable information for the development of efficient integrated pest management programs.