In the trailer for Bloons Monkey City, it is shown that monkeys are under attack from Bloons due to their electrostatic nature. At the start of the series, they are capable of manufacturing Tack Shooters and Bomb Towers. They also exist in the form of Dart Monkeys, which are presumably regular monkeys.
Boomerang Monkeys are native to the Wattle Trees. They were most likely invaded by the Bloons, but managed to hold back the waves. Eventually, they were discovered by the monkeys and joined their team.