•Illumina MiSeq was used for analysis of biofilm on the stelae of the Beishiku Temple. •The microbial communities colonizing the stelae including lichen, bacteria, fungi, algae were characterized. •Temporal variation in bacterial community was mainly driven by climate factors (temperature, precipitation and wind speed). •Some fungi were lichenized type and related to lichens. •The pH correlated with increased diversity of bacteria and algae. Climate and environmental conditions are the main driving factors that are responsible for the biological colonization and deterioration of stone heritage materials, especially for open-air sites. It is critical to determine the relationships among climate, microbial communities, and potential biodeterioration to conserve stone relics. In this study, samples were collected from two severely biodeteriorated stelae that are located in the open air at the Beishiku Temple, China. The genes of 16S/p23S rRNA targeting bacteria and algae and of the ITS1 region for fungi were analysed by using the Illumina MiSeq platform. Additionally, lichens were examined and described. The results showed that the bacterial community compositions varied with seasonal variations and that the dominant phyla were Actinobacteria, Cyanobacteria, and Proteobacteria. Most of the fungi were affiliated with Ascomycota, and some of them were lichenized types and were related to the lichens that had already formed on the stelae. Chlorophyta and Cyanobacteria were the dominant algal groups that inhabited the stelae surfaces. Xanthoria and Lecanora were the most dominant genera, which belong to foliose lichen and crust-like lichen, respectively. PCoA analysis showed that the bacterial and algal community structures, rather than those of fungi, were closely correlated with climate parameters. Temperature, precipitation, and wind speed were the main factors that were associated with changes in bacterial communities, while pH was closely associated with increased diversity of bacteria and algae. This study presents basic insights into the lithic microbial ecology in open-air stone monuments and may guide management decisions for their protection and preventative conservation. Keywords: Climate parameters; Historical stone; Biodeterioration; Bacteria; Fungi; Algae; Lichens.