This paper is about multiple-F0 tracking and the estimation of the number of harmonic source streams in music sound signals. A source stream is understood as generated from a note played by a musical instrument. A note is described by a hidden Markov model (HMM) having two states: the attack state and the sustain state. It is proposed to first perform the tracking of F0 candidates using a high-order hidden Markov model, based on a forward-backward dynamic programming scheme. The propagated weights are calculated in the forward tracking stage, followed by an iterative tracking of the most likely trajectories in the backward tracking stage. Then, the estimation of the underlying source streams is carried out by means of iteratively pruning the candidate trajectories in a maximum likelihood manner. The proposed system is evaluated by a specially constructed polyphonic music database. Compared with the frame-based estimation systems, the tracking mechanism improves significantly the accuracy rate.