Aims Our objective was to investigate the effects of different light intensities on leaf morphology, photosynthetic capacity, heat dissipation and antioxidant enzyme activities in seedlings of Alnus formosana and A. cremastogyne from a hilly region near Lingyan Mountain in northwestern Sichuan Province in China. We also discuss photosynthetic acclimation and photoprotection strategies in seedlings of the two species --Methods-- Three light regimes of 100%, 56.2% and 12.5% of natural light were simulated to match forest openings, forest gaps and forest canopies, respectively. After more than three months, we measured the parameters of gas exchange, including maximum net photosynthetic rate (Pmax), light saturation point (LSP), light compensation point (LCP), net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), intercellular CO2 concentration (Ci), fluorescent non-photochemical quenching (NPQ), maximum efficiency of PSII photochemistry (Fv/Fm) and light use efficiency (LUE), using a LI-6400 in seedling leaves. We also determined pigment contents per unit leaf area, lamina mass per unit area (LMA) and activity of antioxidant enzymes (superoxide dismutase, catalase and ascorbate peroxidase). --Important findings-- LMA, carotenoid content (Cars), ratio of carotenoid to total chlorophyll (Car/Chl) and activities of superoxide dismutase, catalase and ascorbate peroxidase in leaves increased with the increase of light intensities. Pmax, LSP, LCP and NPQ tended to increase, while the chlorophyll content (Chl) and LUE decreased. However, the Ci decreased with the increase of Pn, Gs and stomatal limitation value (Ls). We speculated that non-stomatal limitation was the main factor that inhibited Pn. Seedlings of the two alder species could acclimate to different light regimes in this study through changing of physiological and morphological traits. Under all light regimes, diurnal photoinhibition of photosynthesis, as judged by Fv/Fm, was significantly more severe in A. cremastogyne than in A. formosana. The acclimation capacity to high light regime was stronger in A. formosana than in A. cremastogyne. With the increase of light intensities, Pmax and antioxidant enzyme activities increased significantly, but not NPQ in A. formosana. The opposite trends occurred in A. cremastogyne. At the same light intensity, thermal dissipation was much lower, but Pmax was much higher in A. formosana than in A. cremastogyne. These results indicated that A. formosana seedlings might adapt resistance to photoinhibition through improving the use of solar energy by higher Pmax and antioxidant enzyme system, while A. cremastogyne seedling avoided photoinhibition mainly through converting excess light energy to heat energy in the form of non-radiative dissipation through the antenna system.