A recent survey of the non-marine diatoms of the South Shetland Islands (southern Atlantic Ocean) resulted in the discovery of two unusual species of the genus Pinnularia, section Distantes. Based on both light and scanning electron microscopical research, both species are described as new species: Pinnularia obaesa sp. nov. and P. australorabenhorstii sp. nov. The morphology of both species is compared to other, similar species of the section Distantes. The most striking feature of P. obaesa is its rather unusual alveoli structure presenting a labyrinth-like network of silica rims superimposed on the areolae. Notes on the ecology and biogeography of both species are added.