There were multiple Cypher Keys for example Supply Ships sheltering in neutral ports used the Tibet Cypher. merchant Raiders used Special Cypher 100. Cypher Bertok was used to communicate with the Naval attache Tokyo. Cypher Freya was used between OKM and naval shore installations. Triton Cypher was used by U-boats in the Indian Ocean.
There were even special Enigma keys created for co-operation between the German and Japanese navies operated on three rotor machines known as T-Enigma under the Tirpitz agreement of 1942 (Tirupitsu to Japanese/JN-18 to USN) The code key for this was originally known as Sumatra and later as Gartenzaun. This was mostly used by German I-class U-boats which sailed to Europe such as I-29 and I-52 for example.
The SS had their own Cypher keys such as Kliest many of which were rarely broken. German Railways had their own Cypher Keys as did various Luftwaffe units. The Kreigsmarine used four rotor Enigma machines as opposed to the three rotor machines of the Luftwaffe.
These were books of Cypher keys relevant for specific days and the way they were used changed as the war progressed. Generally a vessel was only issued with a book of Cypher keys lasting three months. Later in the war Keys would change up to twice per day. They were issued on pink water soluble paper.