The present application discloses a method for resolving harmonic ambiguity and inter-array harmonic tracking. The method allows derivation of a complete set of possible harmonic families given the selection (by an operator) or automatic detection (by an automated algorithm) of a single tone (f.sub.selected) from a frequency spectrum using a novel "ambiguity matrix" approach in which a matrix of all N possible harmonic members and M hypothetical fundamentals is constructed. The ambiguity matrix provides an image of all possible harmonic families associated with a selected tone. The selection of the correct fundamental is then made based on simple comparisons between this image and the set of all possible fundamentals. The ambiguity matrix effectively provides a reduced finite solution space (discrete set of possibilities) in which to unambiguously estimate the correct fundamental.