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Peatlands exhibit highly characteristic ecological traits and are unique complex ecosystems. Nevertheless, knowledge about southern South American peatlands is very limited. In this study, we analyzed species composition of bryophytes and lichens of Southern Hemisphere peatlands, specifically from eight peatlands of Isla Grande de Chiloe (Chiloe Island) in southern Chile (42°–43°S and 75°–73°W). Two kinds of Sphagnum peatlands were studied: natural and anthropogenic peatlands. Our results indicate the existence of clear environmental gradients affecting the structure of bryo-lichenic communities in the Sphagnum peatlands of Chiloe. Canonical correspondence analysis suggests that variation in bryophyte and lichen species composition mainly follows ombrotrophic–minerotrophic and lithotrophic-thalassotrophic gradients. Surface-water chemistry is the most significant factor accounting for changes in floristic composition among our study sites. In contrast to our expectations, bog origin (natural or anthropic) was not the most significant factor accounting for changes in floristic composition among peatlands. Other elements, such as the water source supplying peatlands or the influence of sea spray, were more relevant in the bryo-lichenic flora species occurrence in the peatlands of Chiloe. We also observed clear differences in ecological niches among species in general additive model response curves. Therefore, our results show that despite the origin, the ecology of peatlands follows common rules with peatlands from the Northern Hemisphere.