The Eldeen, often referred to as the winged ones, are the mysterious beings that built an advanced civilization long time ago in Ys series.

They constructed their kingdom on the Atlas continent, which was located to the west of the Canaan Islands. Using the special metal called Emelas, they built many artifacts of tremendous power such as the Black Pearl and the Ark of Napishtim and enjoyed great prosperity.

They were originally no different from humans, but with their advanced technology, they were able to transfer their souls to the advanced winged bodies made of white emelas. These bodies granted them immortality and the innate ability to control black emelas. They used the artifact called the mother of spirits to give birth to children who are naturally born with the bodies of white emelas. It is at this point that they became revered as "the winged ones" by other species.

When the sea level around the Atlas continent began rising, they turned the Ark of Napishtim into a control machine for sea levels in order to protect those without wings such as the Rehda and humans.

Unfortunately, their downfall came from the humans who learned the craft of making emelas from them. While these humans were able to create red, blue, and gold emelas, they were unable to make white and black emelas. The winged ones did not teach them how to make black and white emelas, because they contained a vast amount of power and thus could not be controlled easily. While some humans attempted to make black and white emelas on their own, all they got in the end was ash emelas. Nonetheless, humans would go on to create dragon soldiers, the living weapons of mass destruction made of ash emelas, and use them in their warfare.

Dissatisfied with the powers they had, these humans attempted to steal the secrets of making black and white emelas from the winged ones. After stealing the master key Almarion for the Ark of Napishtim, they infiltrated the Ark and tried to gain knowledge and power from it. Unfortunately, this caused the Ark to go berserk and the sea level skyrocketed, flooding the Atlas continent and the Canaan islands.

While Alma managed to prevent the ark from flooding the entire world by sealing it with her white emelas body, the Atlas continent was destroyed and many winged ones chose to ascend to the heavens. After this incident, only few of the Eldeen civilization survived. Three of these survivors have been confirmed so far.

The twin winged ones in charge of the black pearl, Feena and Reah, went to Esteria. With the six humans who were well-versed in magic, they built the great kingdom of Ys. Unfortunately, some descendants of the humans responsible for the fall of Eldeen, now calling themselves the clan of darkness, invaded Ys in hopes of taking the black pearl for themselves. This caused the portion of the kingdom of Ys to float. The events led to the corruption of the black pearl itself and it is not until 700 years later that the adventurer by the name of Adol Christin comes by and brings complete closure to the disaster. The twin goddesses seal themselves along with the black pearl in hopes that the black pearl may not be used for evil purposes again.

Eldeel, with the Akashic Records and its control key Mask of the Sun, helped the Hero-King Lefance build the prosperous kingdom in the land of Celceta. Using the Akashic Records, Eldeel indirectly guided the people of Celceta for hundred of years. However, after the events in Ys: Memories of Celceta, the Akashic Records get shut down permanently and Eldeel acknowledges the future that humans can develop for themselves and seals himself. This marks the complete end of the Eldeen civilization.

Adol encounters many of the artifacts left behind by the Eldeen civilization in his adventures. He would eventually go onto uncover what happened to this once-great civilization.

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