Zygnematophyceae are main primary producers in polar hydro-terrestrial habitats, characterized by extreme abiotic conditions. They are expected to be strongly impacted by climate change, leading to threats to subpolar and polar ecosystems. Two isolates of Zygnema from a subpolar (Iceland, Zygnema sp. I) and a polar Island (Svalbard, Zygnema sp. B) were compared by their photophysiological performance and phenolic content. A phylogenetic analysis was performed in a newly isolated Zygnema I where also morphology and ultrastructure were characterized. The rbcL sequence of the Icelandic Zygnema I was identical to that of Zygnema V, previously isolated from Svalbard, and phylogenetic analysis placed this strain into Zygnema clade 2. Average width of vegetative filaments (28 ± 0.7 µm) and ultrastructure was similar to closely related Zygnema strains. Zygnema I and Zygnema B were exposed to three different treatment temperatures (15, 20 and 25°C) for two weeks, then photophysiological parameters and cellular phenol contents were acquired. The maximum electron transport rate increased significantly with elevated temperatures, but non-photochemical quenching did not change. Net photosynthetic oxygen production was higher in Zygnema B, but decreased in both strains from 10 to 15°C measuring temperature. Zygnema I showed a significant decrease between 15/25°C-treated cultures above 20°C measuring temperature. The phenolic content did not change significantly with experimental treatments, the spectral absorption at 350 nm was significantly lower in Zygnema B when compared with Zygnema I. Taken together our results indicate that Zygnema B and Zygnema I cannot adapt to elevated temperatures.