Microbialites are usually carbonate-rich structures that result from the interplay of complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here we analyzed the communities associated to microbialites occurring in several crater lakes of the Trans-Mexican volcanic belt along an alkalinity gradient. This data can allow the characterization of the impact of this interaction of biotic and abiotic factors influencing microbialite formation and carbonate precipitation rate that might be also relevant for inorganic carbon sequestration purposes.