Abstract Charophytes are benthic macroalgae that live in fresh and brackish waters. Given the historic deterioration of their habitats and their competitive inferiority relative to tall rooted plants under eutrophic conditions, it is hypothesized that charophytes are among the most threatened autotrophs. Also, it is expected that charophytes with generalist niches and functional traits, such as tolerance of a broad salinity range and large height, should thrive owing to available habitats and stronger competitive ability. These hypotheses were tested comparing the rarity of charophytes in the Nordic countries with other autotrophs and analysing the relationship to species niche specialization and functional traits. A value on a rarity–commonness scale was assigned to each species based on their Red List status. Niche specialization was evaluated by the Outlying Mean Index using a large Danish dataset while traits were derived from the literature. Supporting the hypotheses, 50–87% of charophyte species were Red Listed, which is much greater than for vascular aquatic (30–35%) and terrestrial plants (18–28%). Commonness of charophytes decreased significantly with niche specialization in separate analyses of brackish and freshwater sites. For brackish water species, the most influential parameter determining species distribution was salinity while for freshwater species, alkalinity, lake size and chlorophyll concentration played a major role. Four functional traits: shoot height, salinity tolerance, bulbil production and flexible life cycle duration were significantly positively related to commonness. In conclusion, charophytes contain a larger fraction of threatened species compared with other groups of autotrophs. The few common charophytes are generalists tolerant of a wide range of conditions, while specialists often have short stature, restricted life cycle variability and are rare in the disturbed contemporary landscape. It is thus a conservation priority to delineate accurately the environmental conditions preferred by the threatened species and protect or restore proper habitats. Copyright © 2015 John Wiley & Sons, Ltd.