Cnidarians are the oldest venomous lineage, characterised by a diverse range of proteinaceous toxins found in nematocysts (stinging cells). While the distribution of some gene families that encode toxin proteins have been studied in detail, we know very little about the expression patterns of toxin genes across different tissues within an organism. In this study we examined expression patterns of toxin and toxin-like gene families across three tissue types in the sea anemone Actinia tenebrosa. Tissues were selected as they contain the highest density of nematocysts and included acrorhagi (ring of modified tentacles used in intraspecific aggressive encounters), tentacle (epithelial projections apical aspect and used in predation and defence) and mesenteric filaments (multifunctional morphological structures principally used in digestion). A fully replicated RNA-Seq experiment was performed across the three tissues isolated from nine individuals (three replicate pools of three individuals for each tissue type). Sequencing generated at least 80 million paired-end reads per replicate, while the bioinformatic analysis pipeline consisted of de novo assembly followed by remapping of individual samples to quantify gene expression patterns across the tissue types. Overall we found 24,449 differentially expressed transcripts across the three tissue types of which toxin genes localised to nematocysts were significantly over-represented. Over 200 toxin and toxin-like genes, both widespread and cnidarian specific, were differentially expressed. These results show that the expression profiles of toxin and toxin-like genes are unique to specific tissue types and possibly relate to their different roles in attack, defence and prey capture.