Central Andean Highlands represent a singular environment characterized by various extreme conditions. Among them, peatbogs are exceptional marshy habitats scattered throughout this arid and harsh area. In an effort to understand the patterns of beta diversity, we sampled the benthic macroinvertebrates of thirteen peatbogs and related the biological distance with ecological distance using the GDM (Generalized Dissimilarity Modelling) approach. Variables analyzed were altitude, geographical distance, physical and chemical parameters of the water. A coefficient based on the ordering properties of count data, from the perspective of both sites and taxa, was used to measure the compositional similarity between samples. The most frequent taxa were: Hyallela, Simuliidae, Andesiops, Austrelmis, Podonominae, Protallagma, Trichocorixa, Orthocladiinae and Glossiphonidae. The highest altitudinal record ever for leeches is reported here. Altitude and conductivity contributed greatly to the single ecological predictor of beta diversity. Sampling points can be classified first by altitude (cutoff sets at 4,200 m), which can be considered a surrogate of a regional factor (distinction between Puna and High Andean ecoregions) and then by conductivity (cutoff sets at 135 µS cm-1), which can be considered a proxy of a local factor (distinction between hyperfresh and more mineralized habitats). These results suggest a system of ecological filters acting on them.