- Stone Army
- Soto's Pirate Crew
- The Mechanic (formerly)
- Sky Pirates
- Sons of Garmadon
- Hageman Brothers (formerly)
- Aspheera (formerly)
The following villains below were once inmates of Arkham Asylum, but were moved to Kryptarium after Arkham's destruction.
- Kirk Langstrom
- Poison Ivy
- Kryptarium Prison contains some of the world's most dangerous culprits.
- Original concept art depicted Kryptarium as being constructed around a large spire.
- Kryptarium's design is based on a panopticon prison, a circular prison with cells arranged around a central well, from which prisoners could at all times be observed.
- It is unknown what happened to the prisoners when Harumi and Lord Garmadon took it. They may have simply been off-screen.
- Garmadon was imprisoned in a very special solitary confinement cell that is only accessible by Noble's eye iris and a retractable bridge.
- Skales didn't end up in Kryptarium Prison after being arrested, as he was a sent to Ninjago City's local prison instead. When asked about this this, Tommy Andreasen said, "I don't think Kryptarium existed at the the time. Or it was just a city holding cell."