Expression of stress-related genes was investigated in the marine copepod Acartia tonsa in relation to heat shock at two different salinities (10 and 32‰), and it was furthermore investigated whether experimentally induced epibiont infestation led to elevated expression of stress-related genes. Expression of the genes ferritin, Hsp90 and Hsp70 were analyzed in adult copepods by conducting reverse transcription-quantitative real time PCR (RT-qPCR). The expression of Hsp70 and Hsp90 was significantly up-regulated after heat shock and the expression levels were higher in copepods cultivated at 10‰ salinity seawater than in copepods cultivated at 32‰. Significant up-regulation of ferritin (3.3 fold increase) was observed as a response to infestation with the epibiotic euglenid Colacium vesiculosum. Results suggest that (i) A. tonsa responds more pronounced to thermal shock when cultivated in low salinity seawater (10‰) as compared to optimal salinity seawater (32‰) and (ii) epibiont infestation does cause a measureable physiological response in the host.