A cross-sectional survey of 471 individuals was carried out in a hospital in the rural area of Gambo (Ethiopia). Blood samples were prepared for microscopic observation and collected in filter paper for Seminested-Multiplex PCR (SnM-PCR) and real time PCR (qPCR) testing. The SnM-PCR was considered as the gold standard technique and compared with the rest. Thus, agreement between SnM-PCR and LM was determined by calculating Kappa Statistics and correlation between LM and qPCR quantification was calculated by pair-wise correlation co-efficient.Samples analysed by LM and SnM-PCR were positive for Plasmodium sp. 5.5% and 10.5%, respectively. Sensitivity was 52.2% by LM and 70% by qPCR. Correlation co-efficient between microscopy counts and qPCR densities for Plasmodium vivax was R2？=？0.586. Prevalence was estimated at 7% (95% CI: 4.7–9.3). Plasmodium vivax was the dominant species detected and the difference was statistically significant (χ2？=？5.121 p？<？0.05). The highest prevalence of the parasite (10.9%) was observed in age groups under 15？years old.Accurate malaria diagnostic methods have a great effect in the reduction of the number of malaria-infected individuals. SnM-PCR detection of malaria parasites may be a very useful complement to microscopic examination in order to obtain the real prevalence of each Plasmodium species. Although SnM-PCR shows that it is a good tool for the determination of Plasmodium species, today light microscopy remains the only viabletool for malaria diagnosis in developing countries. Therefore, re-inforcement in the training of microscopists is essential for making the correct diagnosis of malaria. Plasmodium vivax was the predominant species in Gambo, a meso-endemic area for this species.