The current push for malaria elimination requires strong surveillance to ensure the optimal use of intervention resources. Defining parasite population genetic structure can identify operational units for interventions aimed at reducing or eliminating transmission and to guide drug resistance containment strategies. Monitoring imported infections is also critical to determine the feasibility of elimination, and can trigger the reorientation of control efforts from broad-ranging to more targeted activities. Parasite genomic surveillance methods that can achieve these objectives are therefore highly sought after. We have developed approaches for the genomic surveillance of both Plasmodium falciparum and Plasmodium vivax using single nucleotide polymorphism (SNP) barcoding and whole genome sequencing. We have applied these approaches to samples from malaria surveys in Papua New Guinea and Solomon Islands to define transmission dynamics and migration networks, and to track the origins of outbreaks. Integrating this information into malaria control and elimination activities remains a challenge, albeit one that can be overcome. This presentation will cover some of the current limitations to utilising genomic surveillance data in the field, how we are addressing them and recommendations of how these tools can be integrated into malaria control programs.