Here's one of the top hotels around Zamboanga:
Though not in the heart of Zamboanga, you may want to visit famous sights in the larger area like KCC Mall De Zamboanga and Zamboanga City Hall.
If you're planning to stay close to Zamboanga City Hall, you won't have any trouble. About 19 miles from downtown Zamboanga, this historic government building is close to a few great hotels. You can roll out of bed and head straight there from Marcian Garden Hotel (1 mile away). You could also investigate the rooms and amenities at Krishatel Leisure Inn (1 mile away) and Zambo Halal Inn Budget Friendly (2 miles away).