From the Super Mario Wiki
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Some instances of humans are implied. For example, the skeletons of what appear to be humans can be found shackled in chains in several of the sunken ships in the area Gloomy Galleon in the game Donkey Kong 64.
In an early version of Super Mario Sunshine, human citizens were originally going to appear in the game, but were removed for unknown reasons (although one human disguised as a Pianta, Il Piantissimo, is in the game).