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Although charophytes have been studied from South America since the 19th century, large regional gaps in their distribution and manifold taxonomic problems hinder a trans-Andean comparison of charophyte diversity. In total, 14 charophyte species have been previously published for Chile. This number is very low compared to countries east of the Andean barrier. Here we present the results of a series of expeditions that gathered data concerning charophyte distribution in Chile between Patagonia and the Peruvian border. About one-third of the several hundred sites investigated between 2011 and 2013 exhibited rich charophyte communities. Accordingly, the number of species known for Chile has increased to a total of 31 and includes two species (Chara fulgens and Nitella asagrayana) reported from South America for the first time. Our results show some marked differences between charophyte communities west and east of the Andes, notably the absence of the Willdenowia group in the region west of the Andes. Possible reasons for this discrepancy are discussed, and different types of charophyte habitats are characterized in order to widen our knowledge about global distribution and dispersal routes of charophytes.