Ancient transport ships were transport vessels that were used in the Ancient's evacuation to Earth. Many of them made it to Atlantis before the First Siege, but several were caught by the Wraith before they reached Atlantis. They are known to possess weapons as well as a cloaking shield, and can hold at least 300 people. (SGA: "Before I Sleep")
| Capital ships | Alteran ship · Aurora-class · City-ship · Destiny |
| Other ships | Cruiser · Freighter · Puddle Jumper · Science vessel · Seed ship · Shuttle · Transport ship |