Samples of pigments from excavated wall-paintings at the great civilization center of the Greek Bronze Age, Thera, have been analyzed by the non-destructive methods of x-ray fluorescence, x-ray diffraction and mineralogical microscopic examination. The results showed that three types of blue pigment were used, namely the well-known Egyptian blue, glaucophane, which is a sodium magnesium (or iron) aluminum hydroxide silicate which occurs as a natural mineral on Santorini, and a mixture of Egyptian blue and glaucophane. Black pigments were rather puzzling in that some of them are carbon as expected, and some are magnesium compounds. The rest of the pigments are very similar to those previously examined from Mycenae and Knossos.