AbstractPlasmodium vivaxtransmission occurs throughout the tropics and is an emerging threat in areas ofPlasmodium falciparumdecline, causing relapse infections that complicate treatment and control. Targeted sequencing forP. falciparumhas been widely deployed to detect population structure and the geographic spread of antimalarial and diagnostic resistance. However, there are fewer such tools forP. vivax. Leveraging global variation data, we designed four molecular inversion probe (MIP) genotyping panels targeting geographically differentiating SNPs, neutral SNPs, putative antimalarial resistance genes, and vaccine candidate genes. We deployed these MIP panels on 866 infections from the Peruvian Amazon and identified transmission networks with clonality (IBD>0.99), copy number variation inPvdbpand multiplePvrbps, fixation of putative antimalarial resistance, and balancing selection in 13 vaccine candidate genes. Our MIP panels are the broadest genotyping panel currently available and are poised for successful deployment in other regions ofP. vivaxtransmission.