Malaria still becomes a public health problem in Indonesia although has declined the last decades. The incidences of malaria in Banyumas shows unstable transmission and still risk of epidemic . Thus, the spatial and temporal distribution is required as part of efforts towards the elimination of malaria in Banyumas. Temporal spatial statistical methods is used to identify a group of malaria incidence at the district level. Purely spatial clusters of malaria incidence from 2004 to 2015 shows that the disease is not distributed randomly in the study area. A total of nine districts of high risk is determined by analysis of Moran's I. The analysis showed that by the Moran's I test, there is spatial autocorrelation found in the percentage malaria incidence from 2004 to 2015 in Banyumas. The use of the model can provide a means to detect the spatial distribution, temporal, and spatiotemporal malaria, as well as to identify areas of high risk of malaria. This research may help in prioritizing resources on high-risk areas for malaria control in the future and towards the elimination of malaria in Banyumas.