There is limited knowledge available on the thermal acclimation processes for bryophytes, especially when considering variation between populations or sites. This study investigated whether short-term ex situ thermal acclimation of different populations showed patterns of site dependency and whether the maximum quantum yield of PSII (Fv/Fm) could be used as an indicator of adaptation or temperature stress in two bryophyte species: Pleurozium schreberi (Willd. ex Brid.) Mitt. and Racomitrium lanuginosum (Hedw.) Brid. We sought to test the hypothesis that differences in the ability to acclimate to short-term temperature treatment would be revealed as differences in photosystem II maximum yield (Fv/Fm). Thermal treatments were applied to samples from 12 and 11 populations during 12 or 13 days in growth chambers and comprised: (1) 10/5 °C; (2) 20/10 °C; (3) 25/15 °C; (4) 30/20 °C (12 hours day/night temperature). In Pleurozium schreberi, there were no significant site-dependent differences before or after the experiment, while site dependencies were clearly shown in Racomitrium lanuginosum throughout the study. Fv/Fm in Pleurozium schreberi decreased at the highest and lowest temperature treatments, which can be interpreted as a stress response, but no similar trends were shown by Racomitrium lanuginosum.