Background: Long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) are essential to malaria control, but are threatened by insecticide resistance. This thesis aimed to: 1) investigate malaria vector species collected indoor and outdoor using different methods; 2) describe species composition of Anopheles vectors collected from different areas; 3) determine susceptibility of Anopheles to pyrethroid insecticides, and 4) evaluate the association between genotypic markers of pyrethroid resistance and mosquito survival. Methods: Between October 2011 and November 2021, mosquitoes were collected from 13 sites across Uganda – indoors: human landing catches (HLC), CDC light traps (CDC LT) and prokopack aspirators; outdoors – HLCs and pit traps. Implementation of vector control, including LLINs only and LLINs + IRS, differed across time and space. Anopheles species composition was assessed using PCR. Standard WHO tube assays were done for permethrin and deltamethrin, with and without piperonyl butoxide (PBO). Mosquitoes were genotyped for Vgsc-L995S/L1014S and Vgsc-L995F/L1014F, Cyp6aa1, Cyp6p4, ZZB-TE, Cyp4j5, and Coeae1d using locked nucleic acid (LNA) and TaqMan assays. Results: Overall, 165,739 female Anopheles mosquitoes were collected from 13 sites using different collection methods. Of these, 160,657 were collected using CDC light traps (objectives 1 and 3), 349 using prokopack aspirators, 746 using human landing catches (indoor and outdoor), 1,234 using pit traps and 2,753 using larval collections. In the assessment of the impact of different mosquito collection methods, the vector density (mosquitoes per unit collection) using CDC light traps was 4.24 compared to 2.96 using indoor HLCs (4.24 vs 2.96, density ratio [DR] 0.70, 95% CIs 0.63–0.77, p < 0.001) and 4.24 compared to 1.82 using prokopacks (4.24 vs 1.82, DR 0.43, 95% CIs 0.37–0.49, p < 0.001). Sporozoite rates were similar between indoor methods, although precision was limited. Considering outdoor collections, the vector density was 3.53 using HLCs compared to 6.43 using pit traps (3.53 vs 6.43, DR 1.82, 95% CIs 1.61–2.05, p < 0.001). However, the sporozoite rate using pit trap collections was significantly lower at 0.004 compared to 0.018 using outdoor HLCs (0.018 vs 0.004, rate ratio [RR] 0.23, 95% CIs 0.07–0.75, p = 0.008). Prokopacks collected a higher proportion of Anopheles funestus (75.0%) than indoor HLCs (25.8%), while pit traps collected a higher proportion of Anopheles arabiensis (84.3%) than outdoor HLCs (36.9%) At least 158,095 female Anopheles mosquitoes were collected from 3 sites with varying malaria transmission intensities to assess the impact of control interventions. In the low transmission site, LLIN distribution was associated with a decline in Anopheles funestus vector density (0.07 vs 0.02 mosquitoes per house per night, density ratio [DR] 0.34, 95% CI: 0.18–0.65, p = 0.001), but not in Anopheles gambiae s.s. (hereafter An. gambiae) or Anopheles arabiensis. In the moderate transmission site, over 98% of mosquitoes were An. gambiae and LLIN distribution was associated with a decline in An. gambiae vector density (4.00 vs 2.46, DR 0.68, 95% CI: 0.49–0.94, p = 0.02). In the high transmission site, the combination of LLINs and multiple rounds of IRS was associated with significantly lower density of An. gambiae (28.0 vs 0.17, DR 0.004, 95% CI: 0.002–0.009, p < 0.001), and An. funestus sensu lato (s.l.) (3.90 vs 0.006, DR 0.001, 95% CI: 0.0005–0.004, p < 0.001), with a less pronounced decline in An. arabiensis (9.18 vs 2.00, DR 0.15 95% CI: 0.07–0.33, p < 0.001). In total, 2,753 An. gambiae s.l. were subjected to phenotype bioassays. Overall, mortality rates in An. gambiae and An. arabiensis following exposure to pyrethroids were 18.8% (148/788) and 74.6% (912/1,222) respectively. Pre-exposure to PBO resulted in higher mortality for both An. gambiae (permethrin: 12.9% to 56.5%; deltamethrin: 25.2% to 68.7%), and An. arabiensis (permethrin: 65.5% to 93.3%; deltamethrin: 82.4% to 89.8%). Most An. gambiae had the Vgsc-995S/F mutation (95% frequency) and the Cyp6p4 resistance allele (87%), while the frequency of Cyp4j5 and Coeae1d were lower (52% and 55%, respectively). Conclusions: The density and species of mosquitoes collected with alternative methods varied, reflecting the feeding and resting characteristics of the common vectors and the different collection approaches. LLIN distribution was associated with reductions in An. funestus s.l. in the lowest transmission site and An. gambiae in the moderate transmission site. In the high transmission site, a combination of LLINs and IRS and multiple rounds of IRS was associated with the significant reduction of An. gambiae and An. funestus s.l. Following IRS, An. arabiensis, a behaviorally resilient vector, was the predominant species. Resistance to pyrethroids was widespread in the study area, and the mortality rate was higher in An. arabiensis compared to An. gambiae. Further surveillance of insecticide resistance and assessment of correlations between genotypic markers and phenotypic outcomes are needed to better understand mechanisms of pyrethroid resistance in conferring resistance to guide vector control.