The spatial distribution of rotifers in the aquatic ecosystems of the Yucatán peninsula is unclear. The peninsula is a karstic platform with heavy anthropogenic activity that presently puts pressure on and increases the fragmentation of aquatic systems. As the distribution of rotifers is unknown in this region, this study was performed to model spatial distribution of rotifers. Based on the analysis of their absence and presence in aquatic systems, using data from specimens collected in the field and bibliographic information from 1997 to 2018, our goal was to provide protection agencies as well as local and regional users with information on the distribution of microorganisms in the aquatic systems. With this material, an 877-record database with was produced. The bioregion outlined is an area in which 45 genera and 140 species of been observed; the study area contains 47.85% of all the rotifer species reported in Mexico. The essential genera in this bioregion are Brachionus with nine species, Keratella with three and Lecane with 44. In these three genera, we observed two morphotypes of rotifers: a small type in the southern zone and a large type in the northern zone.