A surface-sediment survey of pigments in 100 lakes in the Scandes Mountains, northern Sweden, was combined with a reconstruction of Holocene sedimentary pigments from Lake Seukokjaure to assess the major factors regulating phototrophic communities, and how these controls may have changed during the period from the deglaciation (~9700 cal. years BP) to the present. The study area covers a pronounced gradient of temperature and precipitation, and encompasses the subarctic tree line, an important ecotonal boundary in this region. Lake Seukokjaure is located in a presently treeless basin close to the modern tree line. The spatial survey of sedimentary pigments was analyzed using principle components analysis (PCA) and redundancy analysis (RDA). PCA explained 73-83% of variance in pigment abundance and composition, whereas RDA explained 22-32% of variation in fossil assemblages. Dissolved organic carbon (DOC) content of lake water, sediment d¹³C, maximum lake depth, elevation and lake-water conductivity were all identified as environmental variables with significant association with pigment abundances in the spatial survey, although phototrophic communities of lakes situated in different vegetation zones (alpine, birch, conifer/birch) were incompletely distinguished by the ordinations. In the RDAs, the primary pigment variability occurred along a production gradient that was correlated negatively to water-column DOC content and d¹³C signature of sediments. This pattern suggested that the important controls of primary production were light regime and terrestrial supplies of ¹³C-depleted carbon. In contrast, depth, elevation and conductivity were found to be more important for the differentiation of the phototrophic community composition. Application of these spatial survey results to the Holocene sediment record of Lake Seukokjaure demonstrated the importance of DOC for the temporal development of the lake, from an early state of high production to a period of slight oligotrophication. In general, the algal changes were regulated by the interaction of DOC and conductivity, although transitions in the phototrophic community during the late Holocene were less easily interpreted. Terrestrial vegetation development thus appears to be of utmost importance for the regulation of primary production in oligotrophic alpine and subarctic lakes and climate impacts on lakes, whereas other basin-specific factors may control the ontogeny of algal community composition.