Fluorescence techniques have been extensively used for the detection of photoautotrophic organisms. In particular, fluorescence lidars have been successfully employed for the detection and identification of phytoplankton in sea water and, more recently, have been regarded as powerful tools for vegetation monitoring, especially as for the evaluation of forest decline. In this paper the fluorescence lidar technique is proposed as a new tool for the remote monitoring of photoautotrophic biodeteriogens on surfaces of historical monuments. The use of fluorescence lidars can remotely detect photoautotrophic organisms on monuments and, with a suitable spectral resolution, identify the pigments contained into. The advantages of the fluorescence lidar technique with respect to the traditional methods are manifold and can lead to a fast, extensive control of the stony cultural heritage at low cost. Laboratory and lidar experiments were carried out on different stony materials inoculated with microalgal and cyanobacterial species at different cell concentrations to investigate the potentialities of this technique. The experimental. results presented in this paper include the remote detection of biodeteriogens on stony materials at a previsual growth stage by means of a fluorescence lidar and the identification of the fluorescence features of different pigments.