The emergence of primate malaria known as Plasmodium knowlesi in humans, which is always misdiagnosed by microscopy as P. malariae, has contribute to the needs of nucleic acid based technology to be applied in detection and differentiation of malaria parasites. The target DNA sequence of the 18SrRNA gene was amplified by a nested PCR assay for detection and identification of Plasmodium species in 31 Giemsa-stained blood smears examined as P. malariae. The assay demonstrated three samples identified as positive to genus-specific primers but negative to all species-specific primers. Three cases of misdiagnosed species were detected. The samples were diagnosed as P. malariae microscopically, but detected as P. falciparum by PCR assay. Twenty five out of 31 samples were detected as P. knowlesi. None of the samples diagnosed microscopically as P. malariae were identified as P. malariae with the nested PCR assay. Over 80.6% of all malaria cases in this study showed naturally acquired P. knowlesi infections.