Squirrels are medium-sized rodents from Mobius and Earth. They are characterised by their long teeth, bushy tails, love of nuts, and the need to hibernate in trees. Several important squirrels live on Mobius, making them one of the most popular species:

• Shortfuse the Cybernik is a squirrel who was encase in a Cybernik suit of Megatal and forced to do Doctor Robotnik's bidding. Beforehand, the squirrel (previously known as Shorty) stowed away on a Trooper ship and headed to a Badnik Processing Plant to rescue his friends. The attempt was unsuccessful and Shorty was forced to become the Super Badnik. Fortunately, he had previously damaged the software to brainwash him and he now had his free-will, allowing him to release his friends from their Badnik shells and fight in the resistance against Robotnik. Towards the end of the comic, Shortfuse was permanently released from his suit, but can now wear it whenever he wants thanks to Tekno the Canary.

• Sally Acorn is a character more popular in SatAM and Archie Comics, but has a minor role here. She is one of the Emerald Hill folk and has styled herself as a leader when Sonic is away. She was in charge of the building of a secret hideout and tried to exile Sonic from the Zone when they believed him to be responsible for damaging it. She has since left to become a news reporter and covered events such as the falling of the Death Egg and The Battle For Mobius.

• Tufftee is Sally's little brother who stole a pair of Sonic's Power Sneakers and tried to save his friends in the Marble Zone. Sonic came to his rescue and advised him not to be a hero. He later moved to the Turquoise Hill Zone to assist his friends in fighting Badniks.

• Nutmeg of the Spice Maidens seems to be one, although mother Zorabel is obviously not.

• Other minor squirrels have been seen in the background of stories like Megatox, Zonerunner & The Flock and Badniks Bridge.