Zoo Tycoon 2: Ultimate Collection was the second and final compilation release of Zoo Tycoon 2 and included the base game, Zoo Tycoon 2: Endangered Species, Zoo Tycoon 2: African Adventure, Zoo Tycoon 2: Marine Mania, Zoo Tycoon 2: Extinct Animals and every official download except the Asiatic Black Bear. The collection was released in 2006.
- Zoo Tycoon 2 (30 animals)
- Zoo Tycoon 2: Endangered Species (20 animals)
- Zoo Tycoon 2: African Adventure (20 animals)
- Zoo Tycoon 2: Marine Mania (20 animals)
- Zoo Tycoon 2: Extinct Animals (40 animals including overwrites of Zoo Tycoon 2: Dino Danger Pack animals and extinct research lab failures)
- Addax, Asian Elephant, Black Leopard & Stuffed Prey Dummy, Challenge Pack 1, Guest Fun Pack, Holiday Pack, Musk Ox & Tundra Theme Pack, Scenery Pack, Spring Beautification Pack and Updates for Dino Danger (four animals)
- Total of 134 animals included (out of 135 official animals)