Malaria remains a global health threat. Approximately 97% of the population is at risk in sub-Saharan countries, particularly Nigeria. This study compared the performance of 2 diagnostic methods in assessing malaria endemicity in the rural communities of Ebonyi State, Nigeria. A total of 1,140 study participants were screened for malaria parasite using Rapid Diagnostic Test kits (RDT) in the field, while thick and thin films for microscopy were examined in the laboratory. Our result showed that malaria prevalence was 56.8 by RDT and 38.6% by microscopic test. Age group under 10 years had the highest prevalence of 28.9% (RDT) and 23.6% (microscopy), respectively. The highest prevalence of 19.5% by RDT was recorded in Onicha Local Government Area, while the highest prevalence of 13.4% with microscopy was recorded in Ezza North Local Government Area. The sensitivity and specificity of microscopic examination were both 100%, while those of RDT were 95.5% and 75.9%, respectively.