We compared phytoplankton and phytobenthos pigment strategies in 17 shallow lakes and ponds from northern Canada and Alaska, sampled during mid to late summer. Benthic chlorophyll a concentrations (8–261 mg m⁻²) greatly exceeded those of the phytoplankton (0.008–1.4 mg m⁻²) in all sites. Cyanobacteria dominated the phytobenthos, while green algae and fucoxanthin-groups characterized the plankton. Both communities had higher photoprotection in cold, UV-transparent, high latitude waters. Phytoplankton had higher concentrations of photoprotective carotenoids per unit chlorophyll a than the phytobenthos. The planktonic photoprotective pigments were positively correlated with UV-penetration, and inversely correlated with temperature and coloured dissolved organic matter. A partial redundancy analysis showed that the benthic pigments were related to latitude, area and temperature. The UV-screening compound scytonemin occurred in high concentrations in the phytobenthos and was inversely related to temperature, while benthic carotenoids per unit chlorophyll a showed much lower variability among sites. These differing pigment strategies imply divergent responses to environmental change between the phytobenthos and phytoplankton in high latitude lakes.