| 1. Round | 16/08/2008 | Hansa Rostock II | - | Türkiyemspor Berlin | 3:1 |  |
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| 2. Round | 22/08/2008 | VfL Wolfsburg II | - | Hansa Rostock II | 3:0 | |
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| 3. Round | 30/08/2008 | Hansa Rostock II | - | FC Oberneuland | 1:0 | ||||
| 4. Round | 12/09/2008 | VFC Plauen | - | Hansa Rostock II | 2:0 | |
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| 5. Round | 21/09/2008 | Hansa Rostock II | - | Chemnitzer FC | 0:4 | ||||
| 7. Round | 04/10/2008 | Hansa Rostock II | - | Hannover 96 II | 1:4 | ||||
| 8. Round | 18/10/2008 | VfB Lübeck | - | Hansa Rostock II | 3:3 | |
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| 9. Round | 25/10/2008 | Hansa Rostock II | - | Holstein Kiel | 3:1 | |
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| 10. Round | 29/10/2008 | SV Wilhelmshaven | - | Hansa Rostock II | 2:0 | ||||
| 11. Round | 01/11/2008 | Hansa Rostock II | - | SV Babelsberg 03 | 1:1 | |
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| 12. Round | 09/11/2008 | 1. FC Magdeburg | - | Hansa Rostock II | 2:1 | ||||
| 13. Round | 15/11/2008 | Hansa Rostock II | - | Hallescher FC | 0:1 | ||||
| 14. Round | 22/11/2008 | Energie Cottbus II | - | Hansa Rostock II | 1:8 | |
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| 21. Round | 07/03/2009 | Hansa Rostock II | - | VFC Plauen | 2:0 | ||||
| 22. Round | 14/03/2009 | Chemnitzer FC | - | Hansa Rostock II | 2:0 |
Germany