The easiest arrival is by air. Zamboanga International Airport (ZAM) is on the western edge of the city, ten minutes from downtown by taxi. Philippine Airlines, Cebu Pacific, and PAL Express run daily flights from Manila and Cebu — the Manila flight is about 90 minutes.
Boat services from Manila, Cebu, and other Philippine ports use the Port of Zamboanga at the foot of downtown. Ferries also run south to Basilan (1 hour) and Jolo (Sulu — security situation permitting). Overland from elsewhere in Mindanao is possible but long: the bus from Pagadian is around 5 hours, from Davao closer to 15.