Background: Malaria is a major public health issue. Artemisinin-based combination therapies are the WHO recommended treatment for uncomplicated malaria. Plasmodium malariae and Plasmodium ovale infections are considered underestimated and the effectiveness of artemisinin-based combination treatments against them is poorly documented. The aim of this study was to evaluate the efficacy of dihydroartemisinin-piperaquine against low parasite density Plasmodium malariae and ovale infections.  Methods: DNA was extracted from dried blood spots on filter papers with Chelex®-100 or a column-based extraction method. Species detection and determination was conducted by SYBR Green quantitative PCR targeting the cytochrome b gene (cytb-qPCR) followed by restriction fragment length polymorphism analyses. In total, 241 samples from 53 patients enrolled in a clinical trial were analysed. The obtained molecular data were compared with the microscopy data of the study. Results: Only 69 out of 143 microscopy-positive samples were confirmed as positive by cytb-qPCR. Ninety-three samples were identified as parasite negative by both microscopy and PCR. None of the 36 microscopy-defined coinfections were detected in the molecular analysis. The cytb-qPCR success rate was 72.9% (CI95% 61.4-82.6), 75.0% (CI95% 34.9-96.8) and 14.8% (CI95% 6.9-26.2) for parasite densities above 1000 parasites/ μL, between 600-1000 parasites/ μL and below 600 parasites/ μL, respectively. The observed poor qPCR success rate is most likely due to sample degradation under poor storage conditions. Conclusions: This study highlights the impact on the preservation and quality of Plasmodium genomic DNA on dried blood spots, when filter papers are stored for more than 3 years in tropical conditions.