Malaria has traditionally been a leading public health problem in Equatorial Guinea. After completion, in September 2011, of the integrated set of interventions against malaria launched by the Global Fund Malaria Programme in the mainland area, the epidemiological situation of malaria remains unknown. The aim of this study was to investigate the prevalence rate of malaria and associated factors based on the rapid diagnosis test (RDT) in Bata district, in order to provide evidence that will reinforce the National Malaria Control Programme.