Plasmodium malariae infections are often asymptomatic and long-lasting. Mixed infections are often underdetected in areas where P. malariae, P. vivax, and P. falciparum are coendemic. In this study, we described the occurrence of these species circulating as single or mixed infections in Pará state, Brazil, in the Amazon region, with the purpose of clarifying the impact of misidentification of parasite species based only on morphological description using thick blood smear. By using real-time polymerase chain reaction based on the amplification of the mitochondrial DNA, we detected a prevalence of 46% (58/126) mixed infections with 33.3% P. malariae/P. vivax which were read as P. vivax monoinfections by microscopy detection. Our findings confirmed the high circulation of P. malariae in a malaria endemic area in the Brazilian Amazon region.