The Shinobi Clan is a ninja Clan consisting of Mobian chameleons led by the Bride of Constant Vigil. The Shinobi stronghold is located within caves in the Dragon Kingdom; its exact location is hidden from outsiders. Details of the clan are often lost to rumour and myth, though they're somewhat known for secretive behavior and for hiding traps in plain sight. The clan operates in extreme secret, working under the concept that information is the best weapon. It was one of the four clans forced into serving the Iron Dominion.
Protectors of the Dragon Kingdom
The Shinobi Clan generally serves the forces of good, though they do not act openly. In the past, they attempted to police the Dragon Kingdom and oppose the less virtuous clans; however, due to their small numbers they were nearly eliminated. Following this, the clan adopted more indirect, secretive methods to ensure its survival, often working by observation and gathering intelligence. They maintained these tactics for generations; eventually the Brotherhood of Guardians, who watched over Angel Island and other areas of the world, caught the clan's attention. Feeling that this "powerful, species-centric" group had potential to be dangerous, the clan decided to assign an agent to observe the active Guardian of the time so as to be aware of any worrisome decisions made. (SU: #16)
After the Bride of Four Houses brought an end to the Clan Wars by slaying the leader of the Yagyu Clan and making it her own, Constant Vigil surrendered herself and her clan to the Iron Queen, who used them as part of the Iron Dominion's forces. Despite believing the Iron Queen to be evil, she did so because she feared open opposition would result in the destruction of the Shinobi. However, once it was clear that the Iron Dominion had lost most of its power, the Shinobi Clan felt it safe to break away and aid the opposition. (StH: #201, #202, SU: #16)
- Shinobi is the name of a game series made by SEGA starring a ninja of the same name.
- Shinobi is also the Japanese word for a male ninja.
- The clan banner combines an eye with the infinity symbol.
- A chameleon bearing great resemblance to Liza was seen among the clan and it was heavily implied and later confirmed in a blog by current writer Ian Flynn that the chameleon was indeed Liza. 
- A cancelled idea for "The Chaotix Quest" storyline in SU #46-#49 would have revealed that Liza was not, like Espio and Valdez, a member of the Shinobi Clan by birth. She would instead have joined the clan with Espio's sponsorship after being rejected by the Rainbow Valley Chameleons when she was De-Roboticized. When Espio later contacted the clan for help with Mighty the Armadillo and Ray the Flying Squirrel, a still-training Liza would be dispatched in order to help her overcome her issues with other Mobian Races.
- The reason the Shinobi Clan watches the Brotherhood, may be because of a group of Albion scientists experimenting on the Tasmanian Devils.
- It was strongly implied that Espio is the son of the Bride of Constant Vigil in her first non-flashback appearance, and this was later confirmed.
- Shinobi is the name of an Extreme Gear in Sonic Riders: Zero Garvity.