- Reshiram or Zekrom: The final bosses of the game, these Legendary Pokémon have very low catch rates and can be difficult to defeat without the use of strong Pokémon or strategies.
- Kyurem: Kyurem is another Legendary Pokémon that can be difficult to catch, especially if it is not weakened or frozen before being caught.
- Shiny Pokémon: Shiny Pokémon have a very low encounter rate, and if you are lucky enough to find one, you may want to use the Master Ball to ensure you catch it.
- Event Pokémon: Event Pokémon are Pokémon that can be obtained through special events or distributions. They are often difficult to obtain and you may not have a chance to catch them again if you miss out on the event, so it may be worth using the Master Ball to secure your catch.
Keep in mind that you can only obtain one Master Ball per game, so you should use it carefully and only when you truly need it.