Anopheles melas is an understudied malaria vector with a potential role in malaria transmission on the Bijagós Archipelago of Guinea-Bissau. This study presents the first whole genome sequencing and population genetic analysis for this species from the Bijagós. To our knowledge, this also represents the largest population genetic analysis using WGS data from non-pooled An. melas mosquitoes. WGS was conducted for 30 individual An. melas collected during the peak malaria transmission season in 2019 from four different islands on the Archipelago. Insecticide resistance mutations associated with pyrethroid resistance in An. gambiae s.s. were absent in the An. melas population, and no signatures of selective sweeps were identified in insecticide resistance associated genes. Analysis of structural variants identified a large duplication encompassing the cytochrome-P450 gene cyp9k1. Phylogenetic analysis using publicly available mitochondrial genomes indicated that An. melas from the Bijagós split into two phylogenetic groups due to differentiation on the mitochondrial genome, attributed to the cytochrome C oxidase subunits COX I and COX II, and the NADH dehydrogenase subunits 1, 4, 4L and 5. This study presents novel insights into the population structure and insecticide resistance status of this malaria vector, which are relevant to vector control in the region