•Examination of cyanobacterial compounds as a paleoclimate reconstruction biomarker.•Usage of double-centered interaction matrix analysis and heat-map visualization.•SWE compounds were observed in the loess sediment and BLCs samples.•Potential establishment of SWE as a proxy for UV irradiance.•Potential establishment of MWE as a proxy for general stressful conditions. Loess is the most important archive of Quaternary palaeoclimate evolution, with more thorough and systematic investigations carried out in the past two decades in the Carpathian Basin. Application of novel proxies in loess research could improve the state of knowledge of the past climatic changes. In order to examine the feasibility of cyanobacterial pigments to be used as biomarkers in paleoclimate reconstruction and thereby substantiate the presence of cyanobacterial community during loess accumulation, geochemical evidence of cyanobacteria-specific biomarkers in the sediment is required. In this study structurally different cyanobacterial metabolites were examined for their potential to be used as biomarkers. These compounds included scytonemin wavelength equivalent (SWE) and mycosporine wavelength equivalent (MWE) compounds. The effect of various physico-chemical factors (pH value, temperature and light source) on the production of SWE and MWE compounds in correlation with the nitrogen content of the growth medium was studied. SWE compounds were observed in 8 out of 15 soil and aquatic cyanobacterial strains, while MWE compounds were found in all 15 strains. The results show that exposure to UV light induced a higher synthesis of both pigments. Moreover, the presence of SWE compounds was confirmed in cyanobacterial cultures isolated from biological loess crusts (BLCs) as well as in BLC and loess sediment samples. The potential application of these pigment groups as biomarkers in paleoenvironmental and paleoclimatic reconstruction is discussed.