Odisha, an eastern Indian state, is known to be highly endemic for malaria. The current national malaria control programme uses rapid diagnostic test (RDT) for early diagnosis and prompt treatment of the cases followed by microscopy for the identification of species. But as per the available literatures and from our own experience it is known that microscopy suffers with underestimation of mixed Plasmodium species infection, especially P. malariae and P. ovale. Since PCR has proven to have more sensitivity and specificity and able to detect multiple infection of Plasmodium species, we have made an attempt to find out the prevalence of species of parasites by PCR and compare the results with light microscopy. During this study 1589 individuals presenting with fever from two malaria endemic blocks namely Badampahar and Ghatgaon were investigated. Amongst them 110 cases were found to be PCR positive while 99 were microscopically positive for malaria. Out of the total PCR positive cases 42 cases (38.2%) had P. falciparum, 35 (31.8%) had P. vivax and 10 (9.1%) had P. malariae mono infections, while 23 (20.9 %) cases had mixed infections. Of the total 23 mixed infections 11(10%) were having P. falciparum plus P. vivax and rest 12 (10.9%) cases were having P. malariae mixed with either P. falciparum and /or P. vivax. However microscopically only 1(1.4%) case was found to have P. malariae mono infection and none of the mixed infections harbor P. malariae. Multiple kind lottery model analysis of PCR positive samples demonstrated that P. malariae is not distributed randomly in population when compared by different age groups, gender and season. The study also has shown that PCR is highly effective in screening the severe and asymptomatic malaria cases than LM. The result of this study warrants newer surveillance strategies for case detection and management by the programme.