The marine algal species in the Baltic Sea are few due to the low sea water salinity. One of the few species that can be found is Fucus vesiculosus. Even this species is affected by the low salinity and becomes smaller in size in the Baltic. In present work the photosynthesis of F. vesiculosus in the northern Baltic (Bothnian Sea) was compared to the photosynthesis of F. vesiculosus in the Atlantic. Oxygen evolution was measured before and after exposure to 2.3 W of UV-B (280–320 nm) radiation for 5 h, as well as after 48 h recovery in low light. The plants were kept in their own sea water salinity as well as in a changed salinity, this to examine possible correlations between salinity and photosynthesis. The results show a significant higher initial maximal photosynthesis (P max) for Atlantic plants (10.3 nmol O2 g−1 FW s−1) compared to Baltic plants (4.0 nmol O2 g−1 FW s−1). The Baltic plants were found more sensitive to UV-B with a 40–50% decrease of P max as well as a lower degree of recovery (60–70% compared to 75–95% for the Atlantic plants). The higher salinity (35 psu) had a positive effect on the Baltic F. vesiculosus with increased P max as well as increased tolerance to UV-B. The lower salinity (5 psu) had a negative effect on the Atlantic plants with a decreased P max as well as a lower tolerance to UV-B. Pigment content was found higher in Atlantic F. vesiculosus. The pigment content decreased then the Atlantic plants were transferred to 5 psu. The concentration of Chl a as well as the total content of violaxanthin, diadinoxanthin and zeaxanthin in Baltic plants increased when transferred to 35 psu. The Atlantic F. vesiculosus can not survive the low salinity in the northern Baltic (died within 8 weeks). It is likely that a long time acclimation or adaptation to low salinity has taken place for F. vesiculosus in northern Baltic. If this is an ecotypic or genotypic development it is too early to say.