The Elemental Lighthouses have the four elements of Alchemy sealed away within them. Each one is aligned with a different element. Their respective seals are broken by casting the proper Elemental Stars into the wells at their summits. Long ago the power of the lighthouses gave all those in Weyard the ability to use Psynergy. But the people abused those powers and the lighthouses were shut down by a group Sages. The lighthouses are extremely tall, likely hundreds of meters high. Interestingly, they contain lifts on either side of the summit which lower people to the base of the lighthouse again. The lighthouses are full of puzzles and enemies, these enemies typically resistant to the element of the lighthouse, though not always, and the puzzles often involve the element of the lighthouse, such as puzzles involving water pipes in Mercury Lighthouse. During the Golden Sun games, the player must (depending on which game is being played) attempt to stop the lighthouses from being lit, or light them. There is typically a difficult boss battle when one reaches the top of the lighthouse. Every lighthouse is located near a people or tribe that uses Psynergy akin to the element of the Lighthouse. There is evidence that the lighthouses were built by advanced civilizations before the sealing of Alchemy. The images upon entering Venus Lighthouse of the Lighthouse being built and of a man lifting a block with Psynergy is supportive of this.
When any Adept enters the lighthouse aligned with their element, their Psynergy becomes stronger. In battle, that character gets some PP restored every turn. When a lighthouse is lit, any Adept aligned with the same element becomes stronger, and someone of the apposing element becomes weaker (this only affects the story, such as the first battle with Saturos atop Mercury Lighthouse, and affects nothing in battle). It has also been demonstrated near the end of both games (Saturos and Menardi in Golden Sun, and Kyle, along with Felix and Jenna's parents, in Golden Sun: The Lost Age) that the power of a lit lighthouse can restore the health and Psynergy of people in a near-death state, provided they are an Adept of either the appropriate element or the element that shares a symbiotic relationship with the correct element.
There are four lighthouses:
- Mercury Lighthouse which is aligned with Water and located in northern Angara.
- Venus Lighthouse which is aligned with Earth and located in north eastern Gondowan.
- Jupiter Lighthouse, aligned with Wind and located in Northern Atteka.
- Mars Lighthouse which is aligned with Fire and located in the Northern Reaches.