One of the greatest threats to malaria elimination is the emergence and spread of multidrug resistant malaria. In the Greater Mekong subregion malaria parasites have developed resistance to artemisinin and the key partner drugs found in almost all of the commonly used ACTs. The surveillance of drug-resistant malaria and understanding how far these parasites have spread will be vital to combat and contain this threat. Parasite genotyping has provided important information with which to track emerging drug resistant parasites, define the genetic structure of parasite populations, identify reservoirs of infection and discriminate between imported or locally transmitted parasites. ACREME is working with collaborators at the Wellcome Trust Sanger Institute to develop high throughput systems to genotype P. falciparum and P. vivax, develop in country capacity and applying these to parasite isolates collected from over 50 locations across 12 countries. Our recent studies have highlighted a link between acquired immunity to malaria and emergence of drug resistance and the influence of immunity on treatment response in the context of drug resistance. Ongoing work aims to better understand these interactions and their public health significance, especially in the context of malaria elimination and mass drug administration campaigns.