Seawater temperature, oxygen, salinity and pH are important abiotic factors, changes in which can generate stress in marine organisms. Subtidal and intertidal species, such as the sand dollar Dendraster excentricus, are daily exposed to stressors against which they have developed survival mechanisms to face environmental challenges. Analysing the expression of some key genes in response to stress factors due to changes in temperature and pH, especially in the early stages of development, opens a window of knowledge on the effect that these stressors have on benthos marine organisms. In the present work larvae and post-larvae of D. excentricus were exposed to high temperature and low pH scenarios. Survival, size and gene expression of five genes, involved in both stress response (hsp70 IV and hsp90 beta-like) and biomineralization for skeletogenesis (sm29, sm30A, carbonic anhydrase 14-like and mitochondrial proton/calcium exchanger protein LOC575637), were analysed in 4-, 6-, 8-arms, competent larvae and post-larvae. Survival of stressed larvae and post-larvae presented a significant decrease, up to 37% in some stages. A size reduction of almost 30 μm was observed when larvae were exposed to stressful conditions, except in competent larvae and in post-larvae where no significant changes were detected. After stress treatments, transcripts of hsp90 beta-like were up-regulated in all larval stages but hsp70 IV transcripts were not. Under tested stressful conditions sm29 and sm30A expression was down-regulated in larvae and post-larvae, while carbonic anhydrase 14-like and LOC575637 expressions were up-regulated. It is evident that tolerance to changes in seawater temperature and pH has a direct effect on metabolic functions of D. excentricus larvae and post-larvae, which depends on the developmental stage. If laboratory results are extrapolated to marine ecosystems, it is possible that populations of this structuring organism may be disturbed with subsequent damage to ecosystem balance, until resilient organisms acclimatize and adapt to their changing habitats.