1. Kaido's Devil Fruit
Yonko Kaido of the Hundred Beasts ate a mythical zoan devil fruit that allows him to transform into a dragon or Oni. It is unknown whether Kaido was a dragon that ate an Oni Devil Fruit or an Oni that ate a Dragon Devil Fruit. Either way, he could have eaten a mythical zoan devil fruit, making it unique in its own right.
Kaido's already abnormal strength is further enhanced by this Devil Fruit, and it mainly makes him known as the strongest being in the One Piece full world. Sure, it's glorious enough to top this list as the rarest Devil Fruit in the entire series.
2. Tori Tori No Mi, Model: Phoenix
Another of the mythical zoans, Tori Tori no Mi, Model: Phoenix is the Devil Fruit of Yonko Whitebeard's right hand, Marco. Thanks to this Devil Fruit, Marco earned the nickname 'Marco Phoenix'. Apparently by its name, this Devil Fruit gives Marco the ability to transform into a giant Phoenix.
Along with the relatively high strength and stamina possessed by the Zoans, this Devil Fruit also grants a person the special ability to regenerate from any wound within seconds using the 'tops'. its 'rebirth blue fire'. As such, it is a Devil Fruit without any weaknesses, and is one of the scariest fruits we've seen in the series. According to Kizaru, this Devil Fruit is even rarer than the legendary loggias.