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The Trans‐Mexican Volcanic Belt is recognised as a highly biodiverse zone and we present a study of diatom diversity and species distributions in its lakes. We aimed to identify diatom taxa with the highest regional occupancy, explore diversity at a regional level, identify the main variables associated with species distributions, and present weighted average optima for variables that could provide a valuable reference for future palaeoenvironmental research. We used the relative abundances of diatoms in surficial lake sediments to estimate different diversity metrics and alpha, beta and gamma diversities. Groups of lakes with similar diatom assemblages were identified by means of cluster analysis whereas canonical correspondence analysis (CCA) was used to evaluate the association between diatom composition and climatic, morphometric, hydrochemical and trophic status related variables. Weighted average optima were estimated for salinity and temperature. From a total of 184 diatom taxa, three were endemic to one or two lakes and eight had the largest regional occupancy, two of which were associated with high salinity environments (Stephanocyclus meneghinianus, Nitzschia frustulum) and the rest with freshwater conditions (Aulacoseira ambigua, A. granulata, A. granulata var. angustissima, Discostella stelligera, Fragilaria crotonensis, Achnanthidium minutissimum). Surprisingly, endemic taxa as well as those with high regional occupancy were mostly planktic or epipelic motile forms, with high dispersal potential. Our results showed 13 clusters of lakes with similar diatom assemblages, in close agreement with beta diversity which predicted the presence of 12 communities. There was high species turnover (βSIM = 0.97) and CCA showed not only that the main environmental variable defining these groups was salinity, but also that temperature, precipitation, depth, and soluble reactive phosphorus were meaningful variables. There was no evidence of an altitude–diversity pattern. This study emphasises the strong influence that climatic variables have on species distribution when relatively broad geographical areas, with large climatic gradients are analysed.

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