Malaria incidence has declined in Indonesia for years, but it is still found a foci malaria in forest areas. Rapid Diagnostic Test (RDT) has been used as a diagnostic tool in remote forest areas because other tests are difficult to carry out due to poor infrastructure. Microscopic examination requires expert personnel to determine the right interpretation. The disadvantage of both methods of diagnosis is that they cannot detect the low density of parasites, causing the diagnosis to be missed. For this reason, it is necessary to examine the molecular diagnosis to determine the right species. This cross-sectional study was conducted on 105 people aged 15-64 years in forest malaria endemic areas who were randomly selected. The diagnosis of malaria is established through rapid diagnostic test, microscopic, real-time PCR examination for identification of genus, and multiplex real time PCR for species identification. The performance of multiplex real time PCR, microscopic and RDT was compared and evaluated each other. From 105 blood samples, RDT identified 38 malaria cases, consist of 9 as Plasmodium falciparum infection, 9 as Plasmodium vivax and 20 as mixed infection. Light microscopy identified 9 as P. falciparum infection, 5 as P. vivax infection and 5 as mixed infection. Multiplex real time PCR detected 7 as P. falciparum infection, 6 as P. malariae infection, and 4 as mixed P. vivax and P. malariae infection. Using microscopy as a reference test, real time PCR showed an overall sensitivity of 100% and specificity of 91,9%. Multiplex real time PCR for species P. falciparum had 77,8% sensitivity and specificity of 91,83%. RDTs sensitivity of 94,7% and specificity of 76,4%. Using multiplex real time PCR as a reference, microscopy had shown better performance than RDT with sensitivity 73,7% and specificity 100% but RDT had low sensitivity with 14,3% (95% CI 11,45 – 26,87) and specificity of 70,5% (95% CI 65,78-79,67). All three tests performed well to diagnose malaria in this area, but multiplex PCR performed better for detecting Plasmodium species, especially species that produce submicroscopic infections or subpaten infections. Multiplex real-time PCR is the most sensitive malaria diagnostic method that can be used in malaria elimination programs. It has better performance in species identification, species detection with low parasitic density and mixed infection.