This paper looks at the problem of planning an integrated transit system from the viewpoint of optimal fares and zone design. More succinctly, the matter is how to plan an integrated fare system that allows each passenger to travel within different zones with a single zone-based ticket. A 2-level model is given, which is both quite near to real operation practices and makes the planner able to consider various transit firms operating within the same context. The main problem is divided into 2 distinct subproblems: one for the fare problem, and the other for the zone problem, solved sequentially. The fare problem leads to the minimization of an aggregated cost function that is mainly related both to the budget needs of each transit agency, and changing in fare levels for the patronage. The zone problem is solved by a heuristic method which was set up to randomly search for the optimal zone configuration reflecting a given fare policy. Computational test results of the proposed model applied on a real database gathered in the metropolitan area of Florence are also reported.