Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/2009 |  | Giorgos Sarris | DF | |||
| 01/2009 |  | Beto | MF |  | FC Sion | FC Sion |
| 01/2009 | | Nikos Karelis | FW | |||
| 07/2008 | | Zacharias Kavousakis | GK | |||
| 07/2008 | | Dimitrios Geladaris | DF |  | Atromitos | Atromitos |
| 07/2008 | | Maurício | DF |  | Estrela Amadora | Amadora |
| 07/2008 |  | Gernot Plassnegger | MF |  | SK Austria Kärnten | A. Kärnten |
| 07/2008 | | Rogério Martins | MF |  | Asteras Tripolis | Asteras |
| 07/2008 |  | Diego Romano | MF |  | San Martín de Tucumán | CASMT |
| 07/2008 | | Dimitrios Orfanos | FW |  | PAOK Saloniki | PAOK |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/2009 | | Dimitrios Grammozis | MF |  | Omonia Nikosia | Omonia Nikosia |
| 07/2008 |  | Altin Haxhi | MF |  | APOEL Nikosia | APOEL |
| 07/2008 | | Dimitris Kiliaras | MF |  | Panionios GSS | Panionios |
| 07/2008 |  | Clint Mathis | MF |  | Real Salt Lake | Salt Lake |
| 07/2008 |  | Darko Miladin | MF |  | HNK Rijeka | HNK Rijeka |
| 07/2008 |  | Ivan Tasić | MF |  | PS Kalamata | Kalamata |
| 07/2008 | | Georgios Theodoris | MF |  | FSV Frankfurt | FSV Frankf. |
| 07/2008 |  | Dragan Načevski | FW |  | AO Kerkyra | AO Kerkyra |
| 07/2008 | | Perica Ognjenović | FW |  | GS Kallithea | Kallithea |