Anopheles mosquitoes are major malaria vectors, encompassing several species complexes with diverse life histories, transmission risks, and insecticide resistance profiles that challenge malaria control efforts. This study investigated the genetic structure and insecticide resistance profiles of Anopheles gambiae complex mosquitoes in Tanzania. We analysed whole-genome sequence data of 300 mosquitoes collected between 2012-2015 across four regions in northern Tanzania and identified An. gambiae s.s., An. arabiensis, and a distinct taxonomic group that was previously unknown. This distinct taxon has a unique profile of genetic diversity, and appears restricted to the coastal region, and we refer to it as the Pwani molecular form. Analysis of insecticide resistance based on target-site mutations and copy number variations (CNV) showed that these markers were strikingly absent from the Pwani molecular form in contrast to other taxa. Our analysis also revealed a pattern of geographical isolation in the An. gambiae s.s. populations, with samples from north-western site (Muleba) clustering separately from those collected in the north-eastern site (Muheza). These geographically isolated sub-populations also had differing resistance and selection profiles, with An. gambiae s.s. from the north-western site showing genomic evidence of higher resistance to pyrethroids compared to the north-eastern population. Conversely, An. arabiensis showed no geographical population structuring, with a similar insecticide resistance profile across all sampling locations, suggesting unrestricted gene flow. Our findings underscore the need to incorporate genetic data into malaria vector surveillance and control decisions; and could inform the development and deployment of new interventions.