The effect of freezing-thawing alternation on lichen photosynthesis is yet unknown in China. To study the responses of photosynthetic activity (indicated by net photosynthetic rate, Pn) to freezing-thawing cycles and their relationships with water conditions, two species of lichens from Mt. Wulingshan of North China, Flavopunctelia soredica and Peltigera elisabethae, were subjected to 5 freezing-thawing cycles under two thallus water conditions (wet-freezing treatment group: thallus water content > 200% dry weight; dry-freezing group: thallus water content < 20%). The results show that Pn of F. soredica under dry-freeze decreased to 21% as compared with the control after 5 freezing-thawing cycles, and decreased to negative values after 3 wet-freezing cycles. Pn of P. elisabethae decreased to negative values after 5 wet-freezing and dry-freezing cycles. The linear regression analysis between relative Pn and freezing-thawing cycles shows that the slope absolute values decrease in order of wet-freezing F. soredica (58.06) > wet-freezing P. elisabethae (41.01) > dry-freezing P. elisabethae (32.27) > dry-freezing F. soredica (11.44). These results indicate that the photosynthetic activity of both lichens is inhibited by freezing-thawing alternation, and the inhibition extent is dependent on species and thallus water conditions. The increase of water content can intensify the inhibition effects. The difference of photosynthetic response to freezing-thawing cycles between the two lichens may be due to the physiological adaption to different microclimate conditions. P. elisabethae inhabits the shady and moist habitats, while F. soredica occupies more open and drier habitats. F. soredica has higher tolerance to dry and low temperature than P. elisabethae, and its adaptation ability to wet and cold is weaker. Global climate change may have negative effects on the photosynthesis and distribution of lichens through the impacts of alteration of spatio-temporal patterns of freezing-thawing events.