A method and system to identify an isotope provided in a medium to be characterized by an instrumentation system. The identification method includes: measuring at least one reference spectrum for at least two reference isotopes; defining measurement windows for each reference isotope; measuring a measured spectrum on the medium to be characterized; for each reference isotope, calculating for each of the measurement windows a deviation value representing the deviation between the measured spectrum and that of the reference isotope in the measurement window; for each reference isotope, determining from the calculated deviation values a dissimilarity coefficient; and identifying the isotope from the determined dissimilarity coefficients.