Background. In active fault zones, geophysical and geochemical anomalies may have a genotoxic effect on plants growing there, as one of the factors of evolutionary transformation of plant populations. Materials and methods. We applied a cytogenetic analysis to evaluate the genotoxic effect on a Lonicera caerulea L. (blue honeysuckle) natural population in one of the active fault zones in the Altai Mountains. Results. We derived principal cytogenetic indices (i.e., mitotic, prophase, metaphase, anaphase, and telophase indices as well as proportion and range of abnormal mitoses) for meristematic cells of Lonicera caerulea seedlings. The increase in the mitotic activity of meristematic cells from the sites in the local fault zone is connected with the occurrence of the prophase-metaphase block to prevent consequences of an increased cell death (as a result of abnormal mitoses in these phases) and to compensate their losses by a greater number of divisions. We observed the increase in the proportion of abnormal mitoses in samples from almost all the test sites, compared with the control site. This demonstrates the increase in the genotoxic effect of geophysical and geochemical anomalies in these sites. The range of abnormal mitoses of samples from all the test sites shows the increase in the proportion of abnormalities in metaphase, compared to the control site where they can be equally found in metaphase, anaphase, and telophase. Conclusion. The results demonstrate changes of mitotic activity, frequency of occurrence and the spectrum of mitotic anomalies in the root meristem of blue honeysuckle, which grows in conditions with contrast geophysical characteristics.