Background: The importance of accurate diagnosis of all of major diseases cannot be underestimated and efficient laboratory testing is vital to identifying and treating life-threatening illnesses including malaria. In this study, we compared the potential of one of merozoite surface protein genes, PvMSP-3b, for detection of Plasmodium vivax in blood samples by PCR with routinely used marker, ssrRNA gene.Methods: One hundred P. vivax microscopy-positive blood samples were simultaneously tested with two genetic markers, including PvMSP-3b gene and ssrRNA gene by PCR and nestedPCR method, respectively, and their sensitivity and specificity in detection of P. vivax was compared.Results: An important difference was seen in sensitivity between the 2 genetic markers, 100% in case of ssrRNA gene vs. 95% of PvMSP-3b gene. The specificity of the two markers was same (100%). Microscopic diagnoses of thick and thin blood smears was used as "golden standard" method.Conclusion: Due to critical importance of accurate detection of the parasite in malarious area, the PvMSP-3b gene cannot be a suitable marker for detection of P. vivax in blood sample by PCR. More investigations are needed to find other valid markers.