Provided are a signal analyzing apparatus, a signal analyzing method and a computer program wherein an analysis that excludes the subjective of a user can be done and the performance of the analysis can be adjusted. A signal analyzing apparatus (1) generates an intensity distribution of a plurality of particular signals from a spectrum distribution on two-dimensional coordinates measured by a measuring device (3) of an EDX apparatus or the like, and classifies n-dimensional coordinate points on an n-dimensional space, which is defined by a combination of the intensities of n particular signals, into a plurality of clusters by use of an EM algorithm. Further, the signal analyzing apparatus (1) determines the points on the two-dimensional coordinates corresponding to the n-dimensional coordinate points included in each cluster, thereby generating the distribution of a respective spectrum having a respective different shape. The distribution of each spectrum having the respective different shape represents the d
