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Background: The aim of this review was to describe the application of molecular methods in epidemiological aspects of malaria vectors, parasites, and human hosts in Iran and their critical role in malaria control and elimination programs. Methods: Medline, EMBASE, Web of Science, Scopus, and Google Scholar databases were searched systematically for original published papers on PCR, the molecular identification of malaria vectors, the molecular epidemiology of malaria, insecticide resistance, and drug-resistant parasites, in Iran. In total, 51 studies on molecular entomology and 36 studies on molecular parasitology of malaria and three on human host were selected. Results: Molecular methods are essential for improving the detection of malaria infection and monitoring antimalarial drugs and insecticide resistance in malaria elimination settings such as Iran. Conclusion: The application of molecular methods may be of particular interest for malaria control/elimination programs, for monitoring progress towards malaria elimination, and for optimal orientation of program activities.