Laser induced breakdown spectroscopy (LIBS) has surfaced as an attractive alternative to mass spectrometry and wet chemistry methods for chemical identification, driven by its real-time, label-free nature. Rapid analysis needs, especially in high-energy materials and pharmaceutical compounds, have further fueled an increasing number of refinements in LIBS. Yet, isomers are seldom identifiable by LIBS as they generate nearly identical spectra. Here we employ a suite of chemometric approaches to exploit the subtle, but reproducible, differences in LIBS spectra acquired from structural isomers, a set of pyrazoles, to develop a sensitive and reliable segmentation method. We also investigate the possible mechanistic principles (causation) behind such spectral variations and confirm their statistically significant nature that empowers the excellent classification performance.