Moon Stones (月煌石（げっこうせき） gekkouseki ) are meteorites that fall from any of the six moons. They are used as fuel for airships and can be used on weapons when processed.
Each Moon presides over an element or attribute.
- Red: (Nasr) Casts fire and power-enhancing magic. The Red Moon presides over "fire".
- Green: (Ixa'Taka) Casts poison and healing magic. The Green Moon presides over "life".
- Yellow: (Valua) Casts electricity and stat decreasing (power/speed) magic. | The Yellow Moon presides over "lightning".
- Blue: (Yafutoma) Casts wind/water (mainly wind) and speed increasing magic. The Blue Moon presides over "wave".
- Purple: (Glacia, Lands of Ice) Casts frost and ice magic, plus causing confusion and silence. The Purple Moon presides over "ice".
- Silver: (Soltis and the Great Silver Shrine) Casts curing magic of adverse effects and instant-death magic. The Silver Moon presides over "void".
The following chart shows the effectiveness of elemental attacks on enemies with elemental defenses. Enemy elemental defense color can be seen in battle as a border around their portrait when selecting which enemy to attack. Attack element is indicated by row and enemy defense element is indicated by column. The number represents the percentage of regular damage. So, a weapon equipped with the Red Moon Stone will deal 110% damage to a Green enemy, but only 90% to a Blue enemy.
The damage type of regular attacks is decided by which Moon Stone is attached to the weapon. The same goes for Super Moves, except in the cases of Aika and Fina. Aika's Super Moves are always Red and Fina's are always Silver.
- Elcian, even though it is claimed to be a Fire-type enemy, is a black Looper.
- At the discovery Eclipse Point, the Purple Moon is in the state of a Lunar Eclipse.
- It is also predicted that the supernatural power of the Dark Rift caused and causes the effects of Inverse Isle, another discovery.
- At the center of the Dark Rift lies a room with a Black Moon Stone. This suggests the existence of a Black Moon but such a moon is never seen in the game.
- The Legendary Air Pirate Daccat was said to have seen all six Moons will his own eyes. This accomplishment would be incomprehensive if there exists a Black Moon.