Blue Yoshi - He is Green Yoshi's best friend. His abilities are running fast, picking up enemies and items, and accelerating faster, but he can't bounce on spikes, get blue and purple coins, or block projectiles.
Green Yoshi - He is Blue Yoshi's best friend. His abilities are eating enemies with his tongue, ground pounding on spikes, the ability to get yellow, blue, and purple coins from blocks and eaten enemies, and having the magic ability to block most enemy projectiles, but he has slow acceleration, low jumping, and can't hold enemies or items.
Princess Yoshi - She is the princess and heir to the Yoshi Kingdom. Baby Bowser kidnaps her to prevent the prophecy of her mothering a Yoshi that will help Mario defeat Bowser.
King Yoshi - The king of the Yoshi Kingdom, he can only watch as his daughter is carried off by Kamek. He asks the two Yoshi friends to get her back.
The Eight Yoshi Warriors - They are the eight Yoshis who rescued Baby Luigi. This time, they have been kidnapped by Baby Bowser and Kamek.
Kamek - He is the evil archwizard of the Koopa Kingdom. Due to a prophecy that Princess Yoshi's child will grow up to help Mario defeat Bowser, he has kidnapped Princess Yoshi and the Eight Yoshi Warriors. The Eight Yoshi Warriors say that he can make enemies gargantuan and increase their battle prowess, but who knows if they are right?
Baby Bowser - The heir of the Koopa Kingdom is ready to defeat Yoshi again. He is waiting with Princess Yoshi in his Infernal Factory.