Homing endonucleases are always indicated with a prefix that identifies their genomic origin, followed by a hyphen: "I-" for homing endonucleases encoded within an intron, "PI-" (for "protein insert") for those encoded within an intein. Some authors have proposed using the prefix "F-" ("freestanding") for viral enzymes and other natural enzymes not encoded by introns nor inteins, and "H-" ("hybrid") for enzymes synthesized in a laboratory. Next, a three-letter name is derived from the binominal name of the organism, taking one uppercase letter from the genus name and two lowercase letters from the specific name. (Some mixing is usually done for hybrid enzymes.) Finally, a Roman numeral distinguishes different enzymes found in the same organism:
* PI-TliII () is the second-identified enzyme encoded by an intein found in the archaea Thermococcus litoralis.
* H-DreI () is the first synthetic homing endonuclease, created in a laboratory from the enzymes I-DmoI () and I-CreI (), taken respectively from Desulfurococcus mobilis and Chlamydomonas reinhardtii.