The company didn't specify what the "clear signs of cheating" are, but it will most likely target accounts using bots to level up at inhuman speeds, those with skewed location data and other hacks that violate its user guidelines.
"Our main priority with Pokemon GO is to provide a fair, fun, and legitimate game experience for all players. If our system has determined that you cheated, then you will receive an email stating that your account has been terminated," Niantic added.
Niantic recently shut down many third-party Pokemon Go tools like PokeVision, which displayed all of the creatures available for capture in a live map.
If you do believe your account has been terminated incorrectly, you should report it to the Pokemon GO Help Center