Using high-throughput sequencing, we conducted an analysis of the 16S rRNA gene in microbial mats that were obtained from karstic habitats located in the Yucatan Peninsula, Mexico. These mats were collected from diverse locations including floating mats in Sisal, flat mats from Progreso and Ria Lagartos, and Pustular mats from Progreso, enabling a comprehensive investigation of the microbial communities present in these habitats.