Human malaria remains a disease of huge global public health burden and the reported stagnation in malaria control raises further concerns since in the past decade, malaria prevalence had been drastically reduced. Sub-Saharan Africa disproportionately shoulders the global malaria burden given that over 90% of malaria cases in 2018 were recorded in this region. Subsequently malaria is both a health and economic burden in these countries many of which are classified as developing countries by major economic indices.Anopheles gambiae and Anopheles funestus are largely responsible for sustaining malaria transmission in sub-Saharan Africa. These two major malaria vectors exist as complexes and have a wide distribution across the heterogeneous biomes in the sub-Saharan region. In this dissertation we explore two broad themes that will advance our understanding of the vector biology, and specifically aspects of the genetic structure of the two most important malaria vectors in the Afrotropic region. A thorough understanding of the genetic structure of these Anopheline vectors is vital for improvement of the effectiveness of the current vector control strategies while also laying the baseline for novel genetic control strategies like gene drive technology which is likely to supplement the existing vector control tools in the near future.We examined the genetic structure of Anopheles gambiae in the Northwestern Lake Victoria Basin in Uganda. There are over 80 islands within Lake Victoria which constitute the Ssese island archipelago most of which have human habitations partly because of the lucrative fishing industry in Uganda. Our aim was to assess whether Lake Victoria is a significant barrier to gene flow among An gambiae populations in the Lake Victoria Basin and hence assess the potential of the lacustrine islands as potential sites for field trials of gene drives.In this research we expanded on the previous study in this region by i) increasing the number of island and mainland sites sampled ii) using multiple genetic markers iii) re-analyzing data from a previous study to exclude microsat markers within the proximity of inversions and iv) incorporating a temporal aspect by estimating the proportion of genetic variation due to sampling the same site for three time periods. Our study has observed significant genetic isolation of An gambiae populations in lacustrine islands in the Lake Victoria Basin from mainland populations, which is consistent with findings of a previous study. Limited genetic connectedness was also observed among island populations meaning that Lake Victoria is a significant barrier to gene flow. We deem these islands to be potential sites for future genetic control trials.Another theme of this dissertation is focused on Anopheles funestus, an important malaria vector in sub-Saharan Africa that often sustains malaria transmission during the dry season when the population density of An gambiae is low. This vector is generally understudied compared to An gambiae despite its huge medical importance. As such chromosomal inversions in An funestus are poorly studied compared to An gambiae. However, there is sufficient evidence indicating the presence of two chromosomal forms or ecotypes co-occurring in Burkina Faso called 'Kiribina' and 'Folonzo' based on differences in the frequency of common inversion genotypes and linkage disequilibrium among inversion rearrangements within populations. The Kiribina form is characterized by overabundance of standard genotype for these inversions while the Folonzo form is polymorphic. This suggests on going assortative mating between the two ecotypes even when in sympatry. These forms have been observed in other parts of West Africa like Senegal and Cameroon.Since inversions in An funestus are still poorly studied, further studies on these ecotypes is still limited. In addition, the hypothesized roles of inversions (especially in An gambiae) in enhancing behaviors that may impact vector control approaches in sub-Sahara Africa are still largely unknown.One of the major obstacles in studying inversions is the difficulty in rapidly diagnosing inversions. The current traditional cytogenetic karyotyping approaches are sex specific (only half gravid female) and stage specific (4th instar larvae). Consequently, cytogenetic karyotyping is time consuming, may require specialized personnel and difficult to scale up especially in field activities in high mosquito density areas.This study aimed at developing molecular karyotyping assays for common inversions in An funestus, that is, inversions 2Ra, 3Ra and 3Rb. We computationally identified tag SNPs that are in high concordance with inversion genotypes for our inversions of interest. We then validated the candidate tag SNPs using cytogenetically karyotyped samples. Validation of candidate tags was implemented using two high-throughput genotyping platforms; TaqManTM OpenArrayTM and Genotyping in Thousands by Sequencing (amplicon sequencing). Our study observed relatively high concordances between cytogenetic karyotype and molecularly determined karyotype.This study is the first attempt to molecularly karyotype inversions in An funestus, a poorly studied malaria vector. It lays foundation to further explore the vector biology of An funestus and specifically the two forms Kiribina and Folonzo. The tools will also help enhance our understanding of the roles of inversions in adaptive divergence, local adaption as well as other epidemiologically relevant behaviors like resting and oviposition behaviors.In conclusion, the research in this dissertation is vital in building our knowledge base about the vector biology of the most important and widespread vectors of malaria. Knowledge generated in this research will not only help improving existing vector control strategies but also lay a foundation for implementation of novel vector control.