Introduction: malaria is highly endemic in the south-east of Iran and, the prompt assessment of the malaria cases is dependent on sensitive and specific identification of malaria. The aim of this study is to compare light microscopy (LM) and rapid diagnostic test (PfHRP-2/pLDH RDT) with Nested-PCR in the Malaria detection. Method: In this cross-sectional study, all of the suspected malaria individuals, who were referred to Razi Hospital in Saravan, Sistan and Baluchistan were evaluated. Demographic, microscopic, RDT and Nested-PCR data were collected. Nested-PCR as a reference method was compared to other methods. Finally, all the results were analyzed by SPSS software version 20. Results: The sensitivity (Sn), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV), and Kc were reported by LM to be 55.3%, 100%, 100%, 94.3% and 0.671 respectively. Furthermore, the RDT method showed results of 55.3%, 99.6%, 95.4%, 94.3%, and 0.602, respectively. Sn, Sp, PPV, NPV and Kc were reported by LM for p. vivax to be 55.7%, 100%, 100%, 96.2%, and 0.714, respectively. Using the same method for plasmodium falciparum, results were reported to be 25%, 100%, 100%, 97.9%, and 0.393, respectively. Also, the Sn, Sp, PPV, NPV, and Kc by RDT were reported to be 57.7%, 99.6%, 93.7%, 96.2% and 0.695 for p. vivax, respectively. These values for p. falciparum were reported to be 25%, 99.6%, 66.7%, 97.9% and 0.354, respectively. Conclusion: LM and RDT methods have been sensitive and specific in detecting malaria and identifying Vivax species compared to Nested- PCR. By contrast, there was little agreement for P. falciparum using these two methods compared to the nested method.