Monitoring of the cultural heritage state is significant factor for their preservation, the timely restoration, and conservation. The aim of this work is to develop a system for monitoring cultural heritage using new computer technology. The proposed method of image comparison is based on the spectral characteristics of the studied monument. Photographing of the objects is carried out in visible and invisible spectra. Most information on the biological objects can be obtained, for example, when shooting is in the infrared range. Primary image processing, recognition of weathering features, and assessment of their potential hazards as well as evaluating of the overall state of the monument is made using complex computer programs, and the results are accumulated in a special database. This system works as the expert one. It has been shown that the possibility of classification of the main groups of organisms on monuments and assessment of the biofouling area in time is possible by using this method. This method was tested during the survey of ancient petroglyphs in Republic of Khakassia, Tomsk petroglyphs, as well as on a number of historical monuments in St. Petersburg.