The ecological characteristics of benthic diatom genera from lakes and tarns in mountainous areas of Tasmania (76 lakes) and the South Island (65 lakes) and Stewart Island (6 lakes) of New Zealand were investigated. Community composition and diversity were mainly governed by gradients in calcium, pH and the monovalent/divalent ionic (M/D) ratio, with typical acidophilous and calciphilous communities present in both regions. Highest genus diversity occurred in the pH range between 5.5 and 7.5. Marked interregional differences were present in both calciphilous and acidophilous diatom community assemblages, which were at least partially related to variations in the concentration of the chloride, sodium, potassium and humic substances. Acidophilous communities in New Zealand were typically dominated by Frustulia, Brachysira and Kobayasiella, whereas Eunotia and Actinella dominated in Tasmania. Calciphilous communities in New Zealand were characterised by higher relative abundances of the genera Hantzschia, Diploneis, Nupela, Stauroneis and Synedra, whereas their Tasmanian counterparts were typified by the genera Amphora (subgenus Psammamphora), Biremis, Navicula and Psammothidium. The provinciality of the floras underscores the need for continued protection and conservation of high latitude aquatic ecosystems worldwide and in the Australasian region in particular.