Increased levels of insecticide resistance in major malaria vectors such as Anopheles funestus is threatening the continued effectiveness of insecticide-based control programmes. Understanding the ecological factors impacting the spread of resistance alleles in necessary to design suitable resistance management strategies. Here we examined the influence of the highest mountain in West Africa (4,100 meters elevation) on the spread of both metabolic and target-site resistance alleles in An. funestus sensu stricto (s.s) populations. High frequencies of both 296S-Rdl (49% - 90%) and 119F-GSTe2 (67% - 81%) resistance alleles were observed An. funestus s.s. populations across Mount Cameroon. Genetic variability parameters suggested that these resistance markers underwent high levels of polymorphisms with 16 to 12 haplotypes identified respectively. However, neutrality tests were not consistent with recent expansion or resistance genes being under selection. Analysis of the maximum likelihood phylogenetic trees of haplotypes indicated that populations primarily clustered according to resistance patterns, whereas the neighbour joining trees of distances suggested that landscape variations could potentially be associated with the risk of presence and insecticide resistance for malaria vectors. These raise the need for further investigations covering different bioecological zones for a detailed report on current status of insecticide resistance in malaria vectors.