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Aims: Surfaces of cultural monuments are covered with diverse surface-associated microbial assemblages as a result of the substrata such as limestone that the monuments are constructed with as well as the impacts of various environmental pressures on these perpetually exposed structures over a long period. The aim of this study was to examine and compare the epilithic microbial assemblages on two Maya (i.e. Altun Ha and Xunanthunich) sites located in Belize. Methods and results: High-throughput 454 pyrosequencing approach was utilized to elucidate microbial community assemblages on two monuments. Overall, the taxonomic composition of the epilithic assemblages on both sites revealed the numerical dominance by members of the Proteobacteria at 43% and 36.9%, and the Cyanobacteria at 25.8% and 16.6% on Altun Ha and Xunanthunich, respectively. Comparatively, sequence diversity appeared more pronounced among the epilithic assemblages found on Xunanthunich than those on Altun Ha. Conclusions: The occurrence of relatively different epilithic assemblages on the two sites is probably indicative of the variations in the impacts of weathering and other environmental pressures over a long period on both monuments. Significance and impact of study: The results obtained from this study further emphasize the ecological importance of the delineation and elucidation of the bio-geographical distribution and community diversity of epiphytic assemblages on monuments.