Right-clicking on a mountable Pokémon with no item in hand will cause the player to ride the Pokémon. Right-clicking again will dismount. Occasionally, this will not work, in which case it is best simply to recall the Pokémon and send it out again. A saddle will not work and is not needed. Turning must be done with directional keys and can be somewhat difficult. Pokémon will always travel in a straight line in whatever direction their head is aimed; for this a third person view is helpful.
Water mounts typically are able to function on land, including the ability to jump, despite the appearances of some of them. To stay afloat, the jump button must be held, or else the Pokémon will start to sink.
Flying on flying mounts is similar to Creative mode - the jump button must be held in order to ascend. There is no stamina, so flight is unlimited. Flying mounts, with the exception of Drifblim, will be dismounted if flown into water.
The moves Fly and Surf are normally not required to mount Pokémon, but it is possible to make them requirements by setting "Have HM To Ride" to "true" in the Pixelmon config file. This setting will make Pokémon unable to be ridden unless they know either Fly or Surf, rendering most land mounts unusable completely (with the exceptions of Kangaskhan, Nidoking, Nidoqueen, Rhydon, and Tauros, who are able to learn Surf despite not being water mounts). Metagross will also be unusable as a flying mount due to its inability to learn Fly.
It is also possible to disable mounting altogether by setting "Allow Riding" to "false".