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- Air Holes are obvious references to Warp Pipes, from the Super Mario Bros. series.
- Samus can be seen losing at a game of The Legend of Zelda on her Famicom Disk System while flying to Zebes.
- Samus mistakes an Air Hole for a Warp Pipe, and Mario can be seen.
- Certain aspects of the game are similar to the film Aliens. Both involve the female protagonists of the series (Ellen Ripley/Samus Aran) traveling to the homeworld (LV-426/SR388) of a dangerous alien specimen (Xenomorphs/Metroids) to exterminate them. Both films also depict the female protagonist bonding with a last surviving child (a girl nicknamed Newt/the baby), and a final battle with the queen of the alien species (Queen Alien/Queen Metroid). Both Alien 3 and Super Metroid also depict the deaths of both Newt and the baby.
- The Shinespark is based on an attack of the same name from the mecha anime, Getter Robo G.
- The Gadora enemy that first appears in this game has several similarities to the final boss from Kid Icarus, Medusa.
- The Tatori, Jr. in Maridia resemble Buzzy Beetles from the Mario series.
- Mini-Kraid makes a cry similar to the Alien creature.
- The Moon Walk, named after Michael Jackson's dance move of the same name, appears in this game as a technique.
The comic, New Summer Night's Dream, is a reference to Shakespeare's play, A Midsummer Night's Dream.
Super Metroid Japanese strategy guideEdit
The room, A Bridge Too Far, is named after a non-fiction book by Cornelius Ryan.
- Nintendo GameCubes can be seen on the atmospheric stabilizers.
- Certain aspects of the game are similar to the movie Alien Resurrection. For example, the respective female protagonists in Metroid Fusion and Alien Resurrection become a hybrid of themselves and the respective series' alien species. The formerly extinct titular specimens of both franchises are resurrected, and the escape sequence is strikingly similar to the ending of Aliens.
- The Fusion Suit is an unlockable suit in this game, and Metroid is an unlockable bonus.
- The baby is on a (likely unused) texture for a Space Pirate terminal.
- In the Glacier One base there is a Metroid named "Hunter Metroid ds", possibly a reference to Metroid Prime Hunters.
- A man resembling Mario can be seen on the left hand side of the panel where Samus learns that the Chozo have arrived. The character has a hat, gloves, overalls, round nose, boots, mustache and holds a wrench.
- Federation Army Special Ops Battleship VIXIV IV is named after another vessel in the Sakamoto-produced Japanese Game Boy game, X, (predecessor to the Star Fox series) called "Space Tank VIXIV" which departs from an overpopulated Earth in the year XXXX to investigate Tetamus 2. An enhanced version of the vessel also appears in the DSiWare sequel, X-Scape. It is accompanied by a droid called "VIX-529."
- Kreatz nicknames the Space Pirate P-1 "Mr. Crabs", a possible reference to a similarly named character in the television show SpongeBob Squarepants.
- The original Metroid is playable as an unlockable bonus in the game.
- Images from Metroid Fusion can be unlocked by connecting both games with a Nintendo GameCube Game Boy Advance Cable.
- The statue holding the Power Bomb in Chozodia is based on a Chacmool.
- The game's concept of light/dark duality is commonly compared to that of The Legend of Zelda: A Link to the Past. In fact, Retro Studios was assisted by the creators of that game.
- The Sanctuary Fortress rain may have been inspired by the Matrix digital rain.
- Both the Shredder and the Dark Shredder resemble Peahats from The Legend of Zelda series.
- Amorbis is similar to the Graboid from Tremors.
- Sandiggers resemble Lanmolas from A Link to the Past.
- The Grenchlers resemble Shriekers from Tremors 2: Aftershocks.
- Jeff McCloud's surname is a possible reference to Fox McCloud from the Star Fox series.
- He also controls like the Goron from The Legend of Zelda: Majora's Mask.
- Metroid project 'Dread' is mentioned in a scan in the English versions of the game. The Japanese version instead mentions a Dread-Class Turret.
- Mogenar's Hand of Ur attack resembles the Move attack in the Golden Sun series.
- Objects that Samus can grapple shimmer in the environment, like Lara Croft's grapple in the Tomb Raider series.
- If the Ship Bumper Stickers are unlocked, then stickers will appear on Samus' Gunship depending on what save data the player has on their Wii.
- Excite Truck - Orange X over monster truck.
- Wii Sports - Wii Sports logo.
- The Legend of Zelda: Twilight Princess - Triforce emblem on Link's shield and in various parts of Hyrule.
- WarioWare: Smooth Moves - Wario's eyes, nose and moustache, the typical WarioWare logo.
- Wii Play - Wii Play logo.
- Super Paper Mario - Paper Mario's head.
- Mario Party 8 - Star emblem.
- Super Mario Galaxy - Mario "M" symbol.
- Super Smash Bros. Brawl - Smash Ball symbol.
- The Ship Bumper Stickers return in this game, as well as other cameos from Prime, Echoes and Corruption.
- Among the unused stage models in the game is the first boss arena from Ninja Gaiden II, complete with textures for the helipad and helicopter, but no tower. It was used to test the realtime motion cutscene animations. 
- Concept art for the Skultera features a drawing with their mouths open, saying "Buy something will ya!" This is also a line from the first Zelda game.
- The creatures known as Pow bear an almost identical resemblance to Navi of the Legend of Zelda series.
- The RB176 Ferrocrusher strongly resembles the power loader Ripley uses to kill the Queen Alien at the end of Aliens.
- The music in the ending cutscene where Samus leaves the Bottle Ship is similar to the theme of Kalisto from the French film The Rain Children. It was composed by Didier Lockwood. 
- The final line delivered by Samus, "What's past is prologue," is from William Shakespeare's The Tempest. Here, Samus is comparing herself to Antonio and Sebastian, stating that her past could not have produced any result other than combat with her enemies.