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This article is concerned with the estimation of fundamental frequencies in polyphonic signals for the case when the number of sources is known. We propose a new method for joint evaluation of multiple F0 hypotheses based on three physical principles: harmonicity, spectral smoothness and synchronous amplitude evolution within a single source, which are closely related to source segregation in auditory scene analysis. Given the observed spectrum a set of hypothetic partial sequences is derived and an optimal assignment of the observed peaks to the hypothetic sources and noise is performed. Hypothetic partial sequences are then evaluated by a new score function which formulates the guiding principles in a mathematical manner. The algorithm has been tested on a large collection of artificially mixed polyphonic samples and the encouraging results demonstrate the competitive performance of the proposed method.