An algorithm for extracting fundamental frequencies from the sound of a violin duet is presented. The proposed algorithm is composed of two processes: (1) framewise enumeration of candidates for fundamental frequencies using the cepstrum method, and (2) grouping among candidates over its adjacent frames using a hierarchical clustering method. Process (1) includes a subprocess of discriminating between the fundamental component of a tone and harmonic components of the other for duet tones in an octave relation, in particular. This algorithm differs from most of the traditional methods for extracting fundamental frequencies in the fact that it introduces loose constraints on target sounds, but no acoustical model is assumed for the instruments concerned. Thus the algorithm is expected to be applicable to many more types of musical instruments than conventional methods. The correct identification rate evaluated by musical notes was 93% for violin duet sounds in the best case.