The color of quartz and other minerals can be either caused by defects in the crystal structure or by finely dispersed inclusions of other minerals within the crystals. In order to investigate the mineral chemistry and genesis of the famous prase (green quartz) and amethyst association from Serifos Island, Greece, we used electron microprobe analyses and oxygen isotope measurements of quartz. We show that the color of these green quartz crystals is caused by small and acicular amphibole inclusions. Our data also shows that there are two generations of amphibole inclusions within the green quartz crystals, which indicate that the fluid, from which both amphiboles and quartz have crystallized, must have had a change in its chemical composition during the crystallization process. The electron microprobe data also suggests that traces of iron may be responsible for the amethyst coloration. Both quartz varieties are characterized by isotopic compositions that suggest mixing of magmatic and meteoric/marine fluids. The contribution of meteoric fluid is more significant in the final stages and reflects amethyst precipitation under more oxidizing conditions.