One of the most important problems in controlling malaria is the limited access to effective and accurate diagnosis of malaria parasitemia. In the Democratic Republic of Congo (DRC), malaria is one of the leading causes of morbidity and mortality. The purpose of this study was to assess the prevalence of anemia and the relationship with asymptomatic submicroscopic infection. A cross-sectional study was carried out among 1,088 apparently healthy children aged between 6 and 59 months selected at random in the health zone of Miti Murhesa in South Kivu/DRC. Capillary blood was obtained for hemoglobin (Hb) concentration measurement by Hemocue Hb 301. Malaria detection was performed by microscopy and the loop-mediated isothermal amplification (LAMP) assay. Anemia was defined as Hb < 11g/dL. We applied the chi-square test for comparisons, and multiple logistic regression was used to identify the risk factors for anemia and submicroscopic infection. The prevalence of anemia was 39.6%, and the prevalence of parasitemia was 15.9% and 34.0% using microscopy and LAMP test, respectively. Submicroscopic infection was found in 22.3% of the children. The independent risk factors for anemia are infection, children younger than 24 months, low middle-upper arm circumference, and history of illness two weeks before. Otherwise, children with submicroscopic malaria infection have a significantly increased risk for anemia, with a need of transfusion. The prevalence of malaria infection was underestimated, when microscopy was used to diagnose malaria. Children with low parasitemia detected by LAMP but not by microscopy showed a significantly increased prevalence of anemia.