 Abstract Zanzibar has made significant progress towards malaria elimination, but recent stagnation requires novel approaches. Using highly multiplexed droplet digital PCR, DDPCR, based Amplicon sequencing, we were able to sequence 290 samples from five districts covering both main islands. This allowed us to identify fine-scale plasmodium falciparum population structure and info-relatedness and connectivity of infections using an identity by descent, IBD, approach. Despite high genetic diversity, we observe pronounced fine-scale spatial and temporal parasite genetic structure. Clusters of neoclonal infections on Pember indicated persistent local transmission with limited parasite importation, providing an opportunity for local elimination efforts. Additionally, we detected an ad-mixed parasite population on Unguja, and found that a substantial fraction, 2.9 percent, of infections were significantly related to those on the mainland, indicating recent importation. Our study provides a high resolution view of parasite genetic structure across the Zanzibar archipelago and provides actionable insights for prioritizing malaria elimination efforts. This article was authored by Oral Holtzu, Anita Loach, Inajelovina, and others. We are article.tv, links in the description below.