To assess the biological implications of ozone depletion over the Antarctic Peninsula, the ultraviolet (UV) regime of two Antarctic cyanobacterial communities (composed of Leptolyngbya sp. and Phormidium sp.) was manipulated using screens that cut out UV radiation and a lamp which enhanced the dose of UV-B radiation (280–315 nm). The biological response of the cyanobacterial mats was monitored by measurement of chlorophyll fluorescence and pigment concentrations. The Leptolyngbya mat showed significant photochemical inhibition due to increased UV-B relative to photosynthetically active radiation (400–700 nm). The effect of UV on the Phormidium mat was less pronounced and dependent on the method of analysis: significantly lower photochemical yields were observed in UV-enhanced Phormidium mats compared to UV-excluded treatment, but if the yield data relative to the time zero control were considered then no effect of UV enhancement was observed. The Phormidium mat contained over 25 times the absolute concentration of UV-protecting mycosporine-like amino acid (MAA) and double the concentration of carotenoids compared to the Leptolyngbya mat, but the latter contained a higher ratio of carotenoids+MAAs to chlorophyll. There were no significant treatment-related changes in the concentrations of MAA, carotenoids and chlorophyll a in the Phormidium mat. The Leptolyngbya mat showed significantly lower chlorophyll a concentrations under UV enhancement, which could account for the lower photochemical yield in this sample. Our results show that different cyanobacterial species have differing photochemical sensitivity to UV-B radiation, which may confer a subtle advantage to the UV-B tolerant species over the less tolerant type during a period of high UV-B irradiance.