The temperature of the sea surface has been identified as an important parameter of the natural environment, governing processes that occur in the upper ocean. This paper focuses on the analysis of the Sea Surface Temperature (SST) anomalies at the greater area of Cyprus. For that, SST data derived from MODerate-resolution Imaging Spectroradiometer (MODIS) instrument on board both Aqua and Terra sun synchronous satellites were used. A four year period was chosen as a first approach to address and describe this phenomenon. Geographical Information Systems (GIS) has been used as an integrated platform of analysis and presentation in addition of the support of MATLAB (R). The methodology consists of five steps: (i) Collection of MODIS SST imagery, (ii) Development of the digital geo-database; (iii) Model and run the methodology in GIS as a script; (iv) Calculation of SST anomalies; and (v) Visualization of the results.