Testate amoebae are unicellular organisms characterized by a shell-like test. Due to their potential use as bioindicators (and paleoindicators), these organisms have been increasingly studied in the last decade, particularly in temperate latitudes. This study's objective was two-fold: to identify the testate amoeba communities sampled from 29 water bodies in Mexico and to determine if their presence and distribution also made them suitable bioindicators for tropical latitudes. A total of 40 taxa were recorded within 12 genera, and six significant variables -oxygen, pH, depth, temperature, conductivity, and total alkalinity -that explained testate amoeba distribution within and among the water bodies were identified through a canonical correspondence analysis. The Q-mode clusters rendered five assemblages, each named after their respective dominant species: 1) Centropyxis aculeata strain "aculeata" assemblage, 2) Difflugia oblonga strain "bryophila" assemblage, 3) diverse assemblage, 4) Cucurbitella tricuspis assemblage, and 5) Difflugia protaeiformis strain "acuminata" assemblage. We found that Cucurbitella tricuspis and the Difflugia protaeiformis strain "acuminata" have similar ecological preferences to those reported previously for temperate lakes, with the former identified as an indicator of eutrophic environments and the latter as an indicator of low oxygen levels. On the other hand, Centropyxis aculeata strain "aculeata" and Arcella vulgaris seem to indicate adverse conditions, but the source of this environmental stress apparently differs from that reported in temperate latitudes. Although this stress source could not be identified in all cases, our study nonetheless demonstrates that testate amoebae in the water bodies of central Mexico could reveal the presence of environmental stress.