The Bothnian Sea in the northerly part of the Baltic Sea is a geologically recent brackish-water environment, and rapid speciation is occurring in the algal community of the Bothnian Sea. We measured low-temperature fluorescence emission spectra from the Bothnian Sea and the Norwegian Sea ecotypes of Fucus vesiculosus L., a marine macroalga widespread in the Bothnian Sea. Powdered, frozen thallus was used to obtain undistorted emission spectra. The spectra were compared with spectra measured from the newly identified species Fucus radicans Bergström et L. Kautsky, which is a close relative of F. vesiculosus and endemic to the Bothnian Sea. The spectrum of variable fluorescence was used to identify fluorescence peaks originating in PSI and PSII in this chl c–containing alga. The spectra revealed much higher PSII emission, compared to PSI emission, in the Bothnian Sea ecotype of F. vesiculosus than in F. radicans or in the Norwegian Sea ecotype of F. vesiculosus. The results suggest that more light-harvesting chl a/c proteins serve PSII in the Bothnian Sea ecotype of F. vesiculosus than in the two other algal strains. Treatment of the Bothnian Sea ecotype of F. vesiculosus in high salinity (10, 20, and 35 practical salinity units) for 1 week did not lead to spectral changes, indicating that the measured features of the Bothnian Sea F. vesiculosus are stable and not simply a direct result of exposure to low salinity.