Marine macroalgae are key components of rocky shores and provide habitat, food, and shelter for numerous organisms while marine herbivores play an important role in regulating the biomass of seaweeds. To persist in benthic communities, traits evolved in seaweeds to avoid, tolerate, or deter herbivory. An increasing amount of literature confirms that seaweeds often respond to grazers with the induction of chemical defenses. In contrast to terrestrial systems, little is known about temporal dynamics and underlying molecular processes of inducible defenses in seaweeds. A 33 day long induction experiment assessed patterns in temporal variation of anti-herbivory defenses in the brown alga Fucus vesiculosus (bladder wrack) in response to grazing by the isopod Idotea baltica. Every 3 days, two-choice feeding assays with naïve grazers tested whether defenses were induced. Selected samples were used for RNA extraction and microarray hybridizations to determine changes in gene expression patterns. We showed that Fucus palatability varied over time with controls being significantly more consumed than grazed seaweed pieces after 18 and 27 days of previous grazing in the induction period. We observed a significant change in the gene expression of grazed Fucus compared to controls. Isopod grazing up-regulated 536 genes, 340 genes were found to be down-regulated. 21% of all regulated genes were annotated using different databases (e.g. NCBI sequence database, Swiss-Prot protein knowledgebase) and allocated to KOG (Clusters of eukaryotic Orthologous Groups) categories. Isopod grazing and consequential induction of anti-herbivory defenses yielded in up-regulation of the categories ‘intracellular trafficking, secretion, and vesicular transport’ and ‘defense mechanisms’, whereas transcripts involved in photosynthesis were strongly down-regulated. Our data revealed modified gene expression patterns that occurred simultaneously to a reduced palatability in consequence of isopod grazing. The findings represent a first step in understanding cellular processes underlying the induction of anti-herbivory defenses in Fucus vesiculosus.