An algorithm for extracting fundamental frequencies from duet sounds is proposed. The algorithm is based on an acoustical feature that the temporal fluctuation patterns in frequency an power are similar for harmonic components composing a sound for a single musical note played on a single instrument with a single active vibrating source. The algorithm is applied to the sounds of 153 combinations of pair-notes played by a flute duet and a violin duet. Experimental results show that the zone-wize correct identification rate by pitch name are 98% for the flute duet and 95% for the violin duet in the best cases.