When you arrive at the second Geo Gate in the Aqua Ruins, take it to Locca. When you arrive there, take it back to Tsunami Trough - Ocean Cave. When you arrive there, go to your right and walk all the way to the end. There should be a huge oyster here. Cut it open by pressing Circle when you are next to it. It always contains expensive items you can either sell or use, and Mana eggs are almost always found here. The Aqua Egg is found more often, but the occasional Wind Egg or Stone Egg will also appear.

Use the following trick to get a Mana Egg in under two minutes. Upon reaching Light Ruins late in the game, go through until Light Ruins level 2. Enter the Chasm level 2, then back out into Light Ruins level 2 again. Walk in a straight line (avoid the first elevator, where you came from) all the way to the other end to board the elevator up to a secret chamber, where a Mana Egg is sure to appear. Go back to entrance of Chasm to reset the Mana Egg generation. The entire back and forth trip takes just under one and a half minutes. Repeat this as desired.
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