Malaria, a pathology caused by protozoa belonging to the genus Plasmodium, is one of the major threats to global health, with about 300-500 million new clinical cases occurring every year and 1-3 million annual deaths. The recrudescence in the number of fatal cases registered in recent years can be attributed to the diffusion of multi-drug resistant strains of Plasmodium, which make less effective the limited armamentarium of available drugs. Living organisms are a recognized source of potentially bioactive molecules and, among them, marine natural products are emerging as one of the most interesting sources to be exploited for the discovery of new antimalarial compounds. In this article we will report results obtained for a single class of marine metabolites, namely endoperoxide-containing derivatives. Many of these molecules possess a simple six-membered 1,2-dioxygenated ring bearing two or three alkyl/aryl groups of different complexity. They can be divided according to the group linked at one of the two endoperoxide-oxygen bearing carbons: peroxyketal derivatives (methoxy group) or non-peroxyketal derivatives (methyl/ethyl groups). Molecules belonging to these classes show in vitro antimalarial activity in the nanomolar range on chloroquine-resistant strains. A number of investigations gave insights into the mechanism of action of these molecules, suggesting structural changes to optimize their antimalarial activity