Genomics has been a pivotal tool for infectious disease research, especially for malaria where studies into the genome of Plasmodium falciparum have provided insights into population dynamics and determinants of drug resistance. There are six human-infective species of Plasmodium (P. falciparum, P. vivax, P. malariae, P. ovale wallikeri, P. ovale curtisi, P. knowlesi), with most deaths due to P. falciparum infections, and subsequently most research is focussed on this species. Knowledge of the complexity and variability of the Plasmodium spp.genomes, and comparative studies between species, can provide valuable insights into parasite biology, which can aid the development of effective disease control methods. For non-falciparum malaria, the amount of genomic data available is sparse, which this thesis aims to improve, and subsequently provide novel knowledge, specifically regarding two understudied groups of Plasmodium parasites: 1) the first global analysis of P. malariae isolates and 2) an investigation into understudied transmission regions of P. vivax in Brazil. Whole genome sequencing of P. malariae isolates is difficult, partly due to their clinical presentation with low parasitaemias, resulting in difficulties obtaining sufficient DNA for WGS. To overcome this barrier, we initially develop a methodology for selective whole genome amplification (SWGA) of P. malariae isolates which is validated using 19 isolates and demonstrate geographical separation of parasites in addition to single nucleotide polymorphisms (SNPs) within orthologs of genes associated with reduced drug susceptibility. Following this initial pilot study, I proceed to create the first large scale global genomic database of P. malariae isolates, generating high quality WGS data for 155 isolates spanning 4 continents and 25 countries. Using this database, I confirm that P. malariae parasites demonstrate isolation by distance at the continental level between Africa and Asia, with South American isolates related to those from Africa. I identify multiple SNPs within genes associated with drug susceptibility, which can be further validated with in vitro studies. Using the SNPs identified in the global genomic database, I develop an in vitro system using ortholog replacement through CRISPR-Cas9 mediated genome editing in the culture-adapted P. knowlesi A1H1 line to determine the phenotypic effect of genomic variants in the pmdhfr-ts gene. I validate this system for testing dhfr-ts variants using controls for pyrimethamine sensitive and resistant lines, and further demonstrate a pyrimethamine-resistant P. malariae parasite phenotype, based on genomic variants that are seen within the global database. Finally, I investigate P. vivax parasites in the largest genomic database to date (n = 885) spanning 3 continents and 26 countries, with novel sequence data generated for Brazilian isolates across 7 states, 6 of which being previously unstudied regions of P. vivax transmission. I demonstrate isolation by distance in P. vivax parasites and determine potentially significant SNPs within genes suspected to be involved in drug susceptibility, including some signals of positive selection at these loci.Overall, this thesis develops the first platform for P. malariae genomic research and identifies novel loci for investigation into both P. malariae and P. vivax, specifically regarding mutations in candidate genes potentially associated with drug resistance. I build on this by translating genomic candidates into functional research and demonstrate the importance of validating genomic signals.