There is increasing evidence that more genetic variation is present among metazoans than is normally expressed in the phenotype, due in part to the canalization of development. Among teleosts (as in other vertebrates), this genetic variation is often expressed as phenotypic change in response to environmental cues. Using embryonic zebrafish (Danio rerio), this 'hidden' variation is explored in the context of environmental stress by investigating the activity of heat shock protein-90 (HSP90), a cytosolic chaperone that interacts with transcription factors to mediate multiple developmental pathways. Following a 37C heat shock during early somitogenesis (1 hour heat shock, targeting 2-14 somite stages), phenotypic variability was expressed in the lower trunk and tail bud regions, where somite development was reduced or ceased prematurely. In situ hybridization showed that hsp90 was localized to this caudal region 16 hours after heat shock, indicating its potential to coordinate somitic fate. By following transcription and translation of this chaperone, we show that 24 hours following heat shock zebrafish embryos express a protein signature which reflects the RNA message. However, by 48 hours, message and protein are uncoupled; while endogenous gene expression is downregulated, heat-shocked embryos express a discrete segmented protein pattern within the trunk, suggesting regulation of transcription and of translation in response to environmental stress.