Antarctic marine invertebrates are sensitive to temperature fluctuations, and therefore vulnerable to ongoing ocean warming. To investigate molecular responses to heat stress, the benthic isopod Spinoserolis beddardi and the asteroid Diplasterias sp., both adapted to ~0 °C conditions, were used. Organisms were exposed to short-term thermal increments of +3 °C and +7 °C in controlled aquarium experiments. After one week, transcriptomes were sequenced, generating a total of 245 Gb (26 libraries) for Diplasterias sp. and 312 Gb (29 libraries) for S. beddardi. sp. De novo assemblies yielded 392,214 and 438,423 protein-coding transcripts, of which 75,983 and 65,497, respectively, had significant matches to metazoan proteins. S. beddardi showed a faster but limited response, with high transcriptional activation at +3 °C (1,140 up- and 733 down-regulated transcripts) but reduced differential expression at +7 ºC, a temperature that induced mortality and phenotypic stress. Contrarily, Diplasterias sp. displayed broader transcriptional changes increasing with temperature, with 1,175 up- and 1,128 down-regulated transcripts at +7 °C and significant differences between treatments. GO and KEGG enrichment analyses indicated that cellular structure, metabolic pathways, protein folding, and reproductive processes underpin thermal stress responses of both species. This study provides the first comparative transcriptomic insight into the heat stress responses in these two Antarctic benthic invertebrates, offering a framework to assess their resilience under projected ocean warming scenarios.