Modern and fossil populations of a Stephanodiscus Ehrenberg species from June Lake, California (USA) were analysed using light and scanning electron microscopy (SEM). Stephanodiscus valves were a major constituent of almost all analysed samples, often dominating fossil assemblages dating back several thousand years. The most commonly observed Stephanodiscus specimen in the samples bore a striking resemblance to the extinct Late Pliocene species Stephanodiscus klamathensis, particularly under light microscopy. The population size range, ultrastructure, and other defining characteristics closely matched published information on S. klamathensis. However, under SEM, internal views of the specimens from June Lake showed an important difference; specimens lacked valve face fultoportulae, whereas S. klamathensis is characterized by the presence of two valve face fultoportulae, each with three satellite pores near the centre of the valve. Additional differences in valve size range, absence of fultoportulae on the valve face, and the fact that S. klamathensis is an extinct species (observed in diatomites deposited from Late Pliocene to Pleistocene) with no closely related living relatives, necessitates describing this Stephanodiscus as a new species. To date, Stephanodiscus coruscus has been observed only in June Lake, California; most Stephanodiscus that share strong morphological similarities to this species have only been observed in ancient fossil diatomites. Thus, Stephanodiscus coruscus Jeff. R. Stone, Edlund & Streib sp. nov. is not only a new species but also provides a rare glimpse into the likely types of environments that S. klamathensis and other similar ancient Stephanodiscus may have inhabited in the late Pliocene. Character variations between S. coruscus and S. klamathensis reveal potential patterns of evolution in freshwater lineages, such as character loss, over time.