How do you get yellow shard?

Use dive on all the small dark areas of water from lilycove to mossdeep. Just click the a button repeatedly whenever there is a space underwater with no grass until you find shards. When you get a shard, you can take it to a man in a beachhouse near lilycove. He'll give you a stone that matches your shard (a yellow shard will give you a thunder stone, blue is water, green-leaf). Hope this helps.