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The Eastern Indonesian Waters are quite a complex area where this region is traversed by Indonesian Throughflow (ITF) that carries water masses from the Pacific Ocean to the Indian Ocean. The water mass movements have an influence on the condition of the waters in this region, which is the Sea Surface Temperature (SST). The SST has an important role that can control weather and climate. This study aims to analyze the phenomena that occur in the distribution of SST in the Halmahera and Banda Seas. The data used for this research is ten years of SST data (1995-2014) in the Halmahera and Banda Seas. The EOF (Empirical Orthogonal Function) method based on the EVP (Eigen Value Problem) applied to the SST data which produces three main components, that is EOF mode and PC mode respectively. The spatial pattern (EOF modes) shows that SST in the Halmahera and Banda Sea regions, while the temporal pattern (PC modes) shows the cycle of phenomena affecting the SST in these regions. The first mode produces 86.66% variance meaning that the monsoon cycle dominantly affecting SST distribution in the Halmahera and Banda Seas. Whereas in the second mode (6.16%) and the third mode (2.13%) indicating a local cycle and shows that the ENSO cycle has a weakly influence on the SST distribution in the study area. It is also has been clarified by the correlation value between ONI (Oceanic Nino Index) and SST is about -0.245.