Temperature and irradiance are the most important factors affecting marine benthic microalgal photosynthetic rates in temperate intertidal areas. Two temperate benthic diatoms species, Amphora cf. coffeaeformis (C. Agardh) Kütz. and Cocconeis cf. sublittoralis Hendey, were investigated to determine how their photosynthesis responded to temperatures ranging from 5°C to 50°C after short-term exposure (1 h) to a range of irradiance levels (0, 500, and 1,100 μmol photons · m−2 · s−1). Significant differences were observed between the temperature responses of maximum relative electron transport rate (rETRmax), photoacclimation index (Ek), photosynthetic efficiency (α), and effective quantum yield (ΔF/Fm’) in both species. A. coffeaeformis had a greater tolerance to higher temperatures than C. sublittoralis, with nonphotochemical quenching (NPQ) activated at temperatures of 45°C and 50°C. C. sublittoralis, however, demonstrated a more rapid rate of recovery at ambient temperatures. Temperatures between 10°C and 20°C were determined to be optimal for photosynthesis for both species. High temperatures and irradiances caused a greater decrease in ΔF/Fm’ values. These results suggest that the effects of temperature are species specific and that short-term exposure to adverse temperature slows the recovery process, which subsequently leads to photoinhibition.