Geophysical and geochemical anomalies may have a mutagenic effect on plants growing in active fault zones being the factors of evolutionary transformation of plant populations. To test this assumption we evaluated the mutation activity of a Lonicera caerulea natural population in one of the active fault zones in the Altai Mountains. 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. We found that the local geological and geophysical environment (i.e., mineralogical composition of rocks and anomalies of the magnetic field) increases the mitotic activity and the number of abnormal mitoses in the meristematic cells. The results may help to clarify the role of environmental conditions of tectonically active regions in microevolutionary processes.