| Season | 1999–2000 |
|---|---|
| Champions | FC Marco |
| Promoted |
AD Ovarense FC Marco Nacional Funchal |
| Relegated | 12 teams |
|
← 1998–99
2000–01 →
|
|
The 1999–2000 Segunda Divisão season was the 66th season of the competition and the 50th season of recognised third-tier football in Portugal.
The league was contested by 58 teams in 3 divisions with AD Ovarense, FC Marco and Nacional Funchal winning the respective divisional competitions and gaining promotion to the Liga de Honra. The overall championship was won by FC Marco.