Disc I
01. Idumæa [vocals: Marc Almond]
02. Sunset (The Death of Thumbelina)
03. Black Ships In The Sky
04. Then Kill Cæsar
05. Idumæa [vocals: Bonnie "Prince" Billy]
06. This Autistic Imperium Is Nihil Reich
07. The Dissolution Of The Boat "Millions Of Years"
08. Idumæa [vocals: Baby Dee]
09. Bind Your Tortoise Mouth
10. Idumæa [vocals: Antony]
11. Black Ships Seen Last Year South Of Heaven
12. Abba Amma (Babylon Destroyer)
13. Idumæa [vocals: Clodagh Simonds]
14. Black Ships Were Sinking into Idumæa [vocals: Cosey Fanni Tutti]
15. The Beautiful Dancing Dust [vocals: Antony]
16. Idumæa [vocals: Pantaleimon]
17. Vauvauvau (Black Ships In Their Harbour)
18. Idumæa [vocals: David Tibet]
19. Black Ships Ate The Sky
20. Why Cæsar Is Burning Part II
21. Idumæa [vocals: Shirley Collins]

Disc II [bonus] [I Am Black Ship]
01. Eaten Sky [instrumental introduction]
02. Idumæa [alternative vocals: David Tibet]
03. Black Ships In The Sky [alternative version]
04. The Dissolution Of The Boat "Millions Of Years"
05. South Of Heaven [instrumental edit]
06. "Prototypes" Outtake
07. This Autistic Imperium Is Nihil Reich [alternative version]
08. 5 Hypnagogue 5 [alternative version]
09. "Pale Sky" Outttake
10. Black Ship Skips To Armageddon
11. I Am Black Ship
12. Idumæa [alternative vocals II: David Tibet]

Additional info
In order to assist with funding for the album, customers were able to pre-order a copy. These "subscribers" received a mention in the liner notes, as well as a limited edition extra CD, entitled "I Am Black Ship", consisting of alternate versions of the tracks from "Black Ships Ate the Sky".