The understanding of processes that give rise to travertine deposits is important. This is so because of its widespread use as decorative material, but more so in environmental studies due to the significance, by proxy, of travertine in climatology. In this paper, a multifrequency EPR spectroscopy study of the behaviour of an ubiquitary vicariant of Ca in calcite, Mn(II), is presented. EPR spectra were obtained from a natural sample at 9.5 (X-band), 95, 190, and 285GHz, and interpreted through numerical simulation. An analysis of the distribution of the zero-field splitting interaction revealed the source of some unexpected spectral features in the width of the lines in the X-band. By contrast, the homogeneous broadening plays only a minor role. Moreover, field-dependent anisotropies of the Zeeman and hyperfine tensors were observed at higher frequency. On the basis of results garnered in this study, the ZFS interaction of Mn(II) has been ascribed to the microstructural anomalies of the Mn(II) distribution in calcite. This may be considered as the fingerprint of the physical-chemical conditions at the time of travertine deposition. As a consequence, X-band EPR spectroscopy represents a specific tool to investigate the genesis, and to check the homogeneity of Mn(II) distribution in travertines as well as in other calcite-based materials.