Malaria caused by Plasmodium falciparum is a disease that is responsible for 880,000 deaths per year worldwide. Vaccine development has proved difficult and resistance has emerged for most antimalarial drugs. To discover new antimalarial chemotypes, researchers have used a chemical genetic approach to assay 309,474 chemicals. Many chemicals in the library of compounds tested showed potent in vitro activity against drug-resistant P. falciparum strains. A reverse chemical genetic study identified 19 new inhibitors of 4 validated drug targets and 15 novel binders among 61 malarial proteins. Phylochemogenetic profiling in several organisms revealed similarities between Toxoplasma gondii and mammalian cell lines and dissimilarities between P. falciparum and related protozoans. One exemplar compound displayed efficacy in a mouse model. These findings provide the scientific community with new starting points for malaria drug discovery.