Parasite genetic information can reveal crucial information about individual malaria cases, such as markers of drug resistance, as well as information about parasite populations, such as migration, diversity, and responses to interventions. Typically, the availability of genetic data is limited to specific markers; when whole-genome data is obtained, it is limited to a small number of samples, with substantial time lag between collection and data availability. To make genetic epidemiology a successful tool for malaria control and elimination, we have developed a targeted approach that allows comprehensive genotyping of important markers, while using high-throughput methods to drastically reduce the turnaround time. This model has been implemented in the Greater Mekong Subregion (GMS) in a project aimed at providing collaborating national malaria control programmes with timely (<5 weeks) and comprehensive genetic data from field samples collected at public health facilities. To date, GenRe-Mekong partners have collected over 10,000 P. falciparum and P. vivax parasites, and we have genetically characterized ~80% of all parasites. For each participating study, we produce a Genetic Report Card (GRC), which details the genetic profile for each parasite, including genotypes of known molecular markers of drug resistance, complexity of infection, co-infection of other human malaria parasites, and a 101-SNP genetic barcode. Summarized data across all sites produces comprehensive maps of the current state of resistance to artemisinin combination therapy components, as well as previous first-line treatments. In addition, barcode analyses reveal patterns of gene flow and of transmission intensity. Next steps include the expansion of sampling outside of the GMS, improving the reporting of GRCs to increase their effectiveness, and developing improved methods to harness the power of next-generation sequencing. Towards this end, we have developed a system of using amplicon sequencing that can be implemented within laboratories of malaria endemic countries.