The increased frequency of heat waves due to climate change poses a threat to all organisms. Microalgae are the basis of aquatic food webs, and high temperatures have significant impacts on their adaptation and survival rates. Algae respond to environmental changes by modulating their photosynthetic rates and biochemical composition. This study aims to examine the effect of elevated temperature on similar taxa of marine Chlorella originating from different latitudes. Strains from the Antarctic, temperate zone, and the tropics were grown at various temperatures, ranging from 4 to 38, 18 to 38, and 28 to 40 °C, respectively. A pulse-amplitude modulated (PAM) fluorometer was used to assess their photosynthetic responses. Parameters including maximum quantum efficiency (F v/F m), relative electron transport rate (rETR), and light harvesting efficiency (α) were determined from the rapid light curves (RLCs). In addition, the composition of fatty acids was compared to evaluate changes induced by the temperature treatments. Increasing the temperature from 35 to 38 °C for both Antarctic and temperate strains and from 38 to 40 °C for the tropical strain resulted in severe inhibition of photosynthesis and suppressed growth. Although all the strains demonstrated the ability to recover from different stress levels, the tropical strain was able to recover most rapidly while the Antarctic strain had the slowest recovery. The results underline that the thermal threshold for the analysed Chlorella strains temperature ranges between 38 and 40 °C. Furthermore, the analysed strains exhibited different trends in their response to elevated temperatures and recovery capabilities.