| antagonist | episode |
| Anan 7 | |
| Apollo | |
| Balok | |
| Bela Okmyx | |
| Beta XII-A entity | |
| Charles Evans | |
| Claudius Marcus | |
| Deela | |
| dikironium cloud creature | |
| Dr. Janice Lester | |
| Dr. Roger Korby | |
| Dr. Sevrin | |
| Dr. Tristan Adams | |
| Evil Kirk | |
| Flint | |
| Garth of Izar | |
| Gary Mitchell | |
| giant space amoeba | |
| Gorn | |
| Harry Mudd | |
| Kahless, Genghis Khan | |
| Khan Noonien Singh | |
| | antagonist | episode |
| Kor | |
| Kras | |
| Landru | |
| Lazarus | |
| M-113 creature | |
| M-5 multitronic unit | |
| Nomad | |
| Onlies | |
| Parmen | |
| planet killer | |
| Rojan | |
| Romulan Commander | |
| spores | |
| the Companion | |
| the Eymorgs | |
| the horta | |
| the Providers | |
| the Tholians | |
| Thelev | |
| T'Pring | |
| Trelane | |
| Vaal | |
|