Theory: Petey Piranha was created by the Shroobs

Arguments

 * Argument 1: Petey first appears chronologically in Mario & Luigi: Partners in Time, which is also the game that introduces the Shroobs.


 * Argument 2: Petey Piranha is seen in the tunnels beneath the Koopaseum where the Shroobs have gathered. The Shroobs are feeding their enemies to Petey.


 * Argument 3: The Mario Superstar Baseball description states that "A mutation created this boss of the Piranha Plants.” The mutation could’ve been caused by the Shroobs, who are known to have genetically altered many species found in the Mushroom Kingdom for their benefit, such as Swiggler, Spiny Shroopas and Shroob Rexes to name a few.


 * Argument 4: Yoob, another mutated Shroob creation, is used by the Shroobs to prevent the Yoshi’s from helping the Mushroom Kingdom by eating them, similar to what they were using Petey Piranha for.


 * Argument 5: Petey’s voice in Mario & Luigi: Partners in Time is identical to Yoob’s voice.