In the Japanese version of this game, during the opening cutscene after Shadow Mario vanishes from Peach's sight, you can faintly hear Mario saying "Look's like Mario's gonna have to find a job," Toadsworth then asks "Are you starting a new career?" And goes back to to their original conversation. Despite being removed from the International versions, it is spoken in clear English.

In Episode 1: The Road to the Big Windmill, if you skip the Sun Sprite after you defeat the Polluted Piranha Plant and go up the windmill you can battle Petey Piranha. This is the only episode in the entire game that can be skipped. Also, on the way up the windmill a Pianta will say that you are getting ahead of yourself, this is a reference to Super Mario 64 where you can get Power Stars which are not necessarily Mario's current objective.

One of the more well-known things about Super Mario Sunshine before its U.S. release was the "Shine Get!" phrase shown everytime Mario obtained a Shine. Not surprisingly, this fine example of video game Engrish was changed to simply "Shine!" for the English version.

In the beginning of the game, when FLUDD is scanning Mario, there are videos playing in the bottom-left corner of the screen. These videos are Mario fighting Bowser in "Super Mario Bros", Iggy Koopa in "Super Mario World", and Bowser again in "Super Mario 64." In the opposite corner is a list of backwards names which represent past Mario games. Looking closely reveals that both Super Mario Kart and Mario Kart 64 were written with the word KIRT instead of KART.

In Noki Bay, once inside the bottle in the Red Coins in a Bottle level, Mario should fall to the bottom of the bottle and then locate a small rock formation there. If Mario maneuvers into a small square opening towards the back right of the rock formation, he can find a small door inside the opening which is impossible to open. Therefore, the player must rotate the camera to see what is on the other side of the door. In doing so, Mario can see a brown book on the floor of the room behind the impassable door, though its purpose is unknown.

"Isle Delfino" is Italian and literally translates into "Dolphin Island", likely referencing Gamecube's original code name, Project Dolphin (abbreviated as DOL, and can be seen under every Gamecube).

In the beta for the Japanese Version of the game, there are files referencing planned train stations and dialogue involved in obtaining and stamping tickets. Each ticket would take you to one of 15 stations.

In the early beta version of Super Mario Sunshine, Delfino Plaza has a different look than it's later beta and final product.

Il Piantissimo is actually The Running Man from Ocarina of Time/The Postman from Majora's Mask.