| Competition: | Cymru Alliance |
| Season: | 1998–99 |
| Winners: | Flexsys Cefn Druids |
| Relegated: | Mostyn Town |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
The 1998–99 Cymru Alliance was the ninth season of the Cymru Alliance after its establishment in 1990. The league was won by Flexsys Cefn Druids.