| Set | No. | Name | Rarity | |
|---|---|---|---|---|
| ADV-P Promotional cards | 032/ADV-P | Flygon 032 ADV P | None | |
| ADV-P Promotional cards | 033/ADV-P | Flygon 033 ADV P | None | |
| Rulers of the Heavens | 041/054 | Flygon | Holo Rare | |
| PCG-P Promotional cards | 125/PCG-P | Flygon 125 PCG P | None | |
| Mirage Forest | 066/086 | Flygon ex | Holo Rare | |
| Holon Phantom | 003/052 | Flygon Delta Species | Holo Rare | |
| Offense and Defense of the Furthest Ends | 037/068 | Flygon ex Delta Species | Holo Rare | |
| Alter Genesis | 44 | Flygon GX | Double Rare | |
| Black & White Promos | 157 | Flygon | None | |
| Black & White Promos | 168 | Flygon | None | |
| Dragon Storm | 30 | Flygon | ||
| Freeze Bolt | 44 | Flygon | ||
| Gaia Volcano | 54 | Flygon | ||
| Inferno X | 47 | Flygon | Rare | |
| Inferno X | 88 | Flygon | Art Rare | |
| Infinity Zone | 46 | Flygon | Uncommon | |
| Paradise Dragona | 27 | Flygon ex | ||
| Paradise Dragona | 79 | Flygon ex | ||
| Rising Fist | 71 | Flygon | Uncommon | |
| Star Birth | 72 | Flygon V | Double Rare | |
| Star Birth | 110 | Flygon V | Secret Rare | |
| Start Deck 100 | 224 | Flygon |