Centuries ago, Wyverns and humans were at war. However, it was a war that was wrongfully started by the Shadow Lord who lives in the Nether realm. The Shadow Lord attempted to destroy humanity by invoking the Wyvern's wrath. It wasn't until a woman (supposedly Lady Irene), who could commune with the Wyverns, came and revealed the Shadow Lord for what he truly was. However, it was too late to stop it, as the humans, once they had their minds set, nothing could've stopped them. The king at the time continued relentlessly to pursue our realm by sending in warriors of powerful dark magic. Where the king was able to create such powerful dark warriors, is still unknown to this day, but an Elder Wyvern came to the other Elder Wyverns with a proposal to seal what remained of the Wyvern world within their realm. The older Elder Wyvern used a staff to seal the shrine from which you can enter, preventing both worlds from destroying themselves. A few of the Wyvern eggs had been sent to the overworld, which they dwelled in a gemstone cave in the surrounding areas of Phoenix Drop.
As of Season Two, their whereabouts are scattered across Ru'an and the other regions.
Aphmau entered the Wyvern's Lair to get some Wyvern Lair Logs for an old man to build a town. Later, she meets the Elder Wyvern who convinced her not to give the wood to the old man, as it could cause lots of trouble. Gaia also asked her to help her find her children, that were sent to the human world, such as Raven. The old man later turns out to be Zenix in disguise.
At the start of Season Two, the whereabouts of the Wyverns were unknown, as they were scattered around Ru'an and it's surrounding regions, until it was revealed in "Jeweled Cavern" that they were living in a cave on an uncharted island.
It is unknown if they are still living on the island or have moved elsewhere in Season Three.