In light of increasing sea surface temperatures, quantifying the expression of stress- inducible genes in coastal organisms is imperative to identify early biomarkers of thermal stress. In the present study we developed a quantitative PCR (qPCR) assay to test the molecular response to heat stress in the Great Barrier Reef sponge Rhopaloeides odorabile. Suitable reference genes (cod- ing for α-tubulin, 28S rRNA and ubiquitin) were identified among 5 candidates and then used to nor- malise expression of target genes (actin-related protein, calmodulin, ferritin, ubiquitin-conjugating enzyme, heat shock protein 90 (Hsp90) and heat shock protein 40 (Hsp40)) in samples exposed to high temperatures (31 and 32°C) for 1, 3, 14 and 15 d. A rapid down-regulation of most genes (actin- related protein, ferritin, calmodulin and Hsp90) was observed at both temperatures within 24 h, indi- cating an initial shut-down of the sponge's molecular systems in response to thermal stress. The increased expression of Hsp40 and Hsp90 in sponges at 32°C after 1 and 3 d respectively indicates an activation of the heat shock response system and is consistent with their role as chaperones for direct- ing degraded proteins to proteolysis, this last process being sustained by an induction of the ubiqui- tin-conjugating enzyme gene at this temperature. While sponges kept at 32°C only survived for the first 3 d, none of the genes in sponges kept at 31°C were significantly different from those in the 27°C controls after 14 d. This indicates a very strict thermal threshold for R. odorabile between 31 and 32°C and is consistent with previous findings based on sponge necrosis and symbiotic disruptions in this species.