evidence: Malaria transmission and infection risk has decreased in Kenya and cases of the disease are generally not seen in high-elevation regions, such as Nairobi, due to the inability of mosquito vectors to survive at such altitudes. Low-elevation regions, however, such as the Lake Victoria basin and coastal regions along the Indian Ocean, still struggle with high rates of malaria transmission as they provide ideal breeding habitats for Anopheles mosquitoes10,11. Depending on the season, P. falciparum infection rates in the Lake Victoria basin can exceed 40% for those aged 2 to 10 years old12. Due to the size of Lake Victoria, and its location along three country borders with differing government policies concerning the implementation and funding of malaria control programmes, applying any targeted vector control in and around Lake Victoria has proven incredibly difficult4,11. There are multiple inhabited islands within the Kenyan territory of Lake Victoria, such as Mfangano island (population size 26,000) and Ngodhe island (population size 600–1000), which offer a unique opportunity to study malaria elimination strategies and changes in parasite genetic diversity. [...] Our analysis revealed that P. falciparum isolates from the Lake Victoria region of Kenya have distinct ancestral origins, with a high proportion tied to Central and East African lineages, and form a distinct sub-group within East Africa in population structure analyses. Known drug resistance biomarkers were observed in the Lake Victoria isolates at similar frequencies to those of East African parasite populations.