Chlorophyll fluorescence is an effective tool for investigating characteristics of any photosynthesizing organisms and its responses due to different stressors. Here, we have studied a short-term temperature response on two Antarctic green algal lichen species: Umbilicaria antarctica, and Physconia muscigena. We measured slow chlorophyll fluorescence transients in the species during slow a cooling of thallus temperature from 20°C to 5°C with a 10 min. acclimation at each temperature in dark. The measurements were supplemented with saturation pulses for the analysis of chlorophyll fluorescence parameters: maximum yield of PS II photochemistry (FV/FM), effective quantum yield of PS II photochemistry (FPSII) and non-photochemical quenching (NPQ). In response to decreasing thallus temperature, we observed species-specific changes in chlorophyll fluorescence levels P, S, M, T reached during chlorophyll fluorescence transient as well as in the shape of the chlorophyll fluorescence transients. With a decrease in temperature, the time at which M and T chlorophyll fluorescence levels were reached, increased. These changes were attributed to redox state of plastoquinon pool, changes in Calvin-Benson cycle activity, non-photochemical quenching components, state transition in particular. In this study, we present some chlorophyll fluorescence ratios (P/M, M/T, P/T) and chlorophyll fluorescence increase rates (FR1, i.e. O to P, and FR2 - i.e. S to M) as the parameters reflecting direct temperature effects on chloroplastic apparatus of lichen alga sensitively. We proposed that species-specific changes in the slow phase of chlorophyll fluorescence transients could be potentially used as indicators of low temperature effects in photosynthetic apparatus of lichen algal photobionts. Interspecific differences in response to low temperature might be evaluated using the approach as well.