Marine macroalgae represent an important part of coastal ecosystems in temperate and polar areas. Increasing surface UV radiation (UVR) levels due to stratospheric ozone thinning may lead to deleterious effects on the physiology of marine macroalgae. Only few studies concentrate on the response of macroalgal gene expression towards elevated UVR. Analyzing gene expression in marine algae is challenging regarding RNA extraction, enrichment of differentially expressed transcripts and identification of resulting sequences. Thus, we focused on the optimization of the appropriate techniques using the widely distributed green marine macroalga Acrosiphonia arcta. We successfully used a combination of suppression subtractive hybridization (SSH) with microarray-based screening of size-selected cDNAs libraries and were able to substantially improve the outcome compared to standard techniques.