The Elemental Lighthouses comprise four elemental components of the seal placed on Alchemy. Each one is aligned with a different element. When the proper Elemental Stars are cast into the wells at their summits, the Lighthouses' respective Elemental Beacons are lit from the Stars, and these spheres of energy are purified essences of each element that output elemental energy across the world of Weyard.
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.
The Elemental Lighthouses were alight during Weyard's ancient past. At this time, Alchemy-driven wars were being fought, leading the ancients to seal away Alchemy. As part of the process, the Lighthouse Beacons put put out, with the essence of each Lighthouse's element being stored as spherical jewels that became known as the Elemental Stars.
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 originally built by mankind using Psynergy, which happened 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. The descendants of three of these tribes are still present in modern times; however, there is no sign of the Venus-element tribe.
A precarious balance appears to exist between the lighthouses, related to the relationships between the Elements. Early on, a balance is reached when both Mercury and Venus Lighthouses are lit. However, when Jupiter Lighthouse is lit, the corresponding lack of Mars Psynergy combined with the cooling power of Jupiter and Mercury plunge the world into freezing temperatures. Only when Mars Lighthouse, which symbolizes heat, is lit does the climate return to normal.
 Significance to gameplay and plot
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.
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 (the latter only affects the story, such as the first encounter 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.