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In this paper a simulation model for a very used public transportation system in Bogotá (Transmilenio) by means of Petri Nets is presented. The modeling of the system is done using a multiagent approach in order to simulate and analyse the resources involved to supply the passengers' demand in rush hour. Petri Nets are used in order to simplify the complexity of the model graphically to describe the system behaviour. Real data are acquired to make the model more realistic. Furthermore, an experimental methodology is used to verify the accuracy of the proposed model and validate the simulation results.