In the ablation zone of glacier habitats, cryoconite holes are known to harbor diverse microbial communities, including unique diatom floras distinct from those of surrounding aquatic and terrestrial systems. Besides descriptive studies, little is known about the diversity of cryoconite diatoms and their response to environmental stressors, particularly in low-latitude glaciers. This paper documents an extremely diversified diatom community in Antisana Glacier (Ecuador), reporting 278 taxa found in 54 surface holes, although with low individual abundances. Contrary to our expectations, assemblage structure did not respond to water physical or chemical characteristics, nor to cryoconite hole morphology, but to elevation. We demonstrate that elevation is a driver of diatom assemblages. Both alpha diversity (measured as Fisher's index) and species richness (corrected for unequal sample sizes) correlated negatively with elevation, suggesting a replacement toward simplified, poorer communities along this gradient. The taxonomic composition also changed significantly, as revealed by multivariate statistics. In summary, cryoconite holes are sites of high taxonomic diversity composed of taxa that are allochthonous in origin.