Global warming is intensifying interest in the mechanisms enabling ectothermic animals to adjust physiological performance and cope with temperature change. Here we show that embryonic temperature can have dramatic and persistent effects on thermal acclimation capacity at multiple levels of biological organization. Zebrafish embryos were incubated until hatching at control temperature (T E = 27°C) or near the extremes for normal development (T E = 22°C or 32°C) and were then raised to adulthood under common conditions at 27°C. Short-term temperature challenge affected aerobic exercise performance (U crit ), but each T E group had reduced thermal sensitivity at its respective T E . In contrast, unexpected differences arose after long-term acclimation to 16°C, when performance in the cold was ∼20% higher in both 32°C and 22°C T E groups compared with 27°C T E controls. Differences in performance after acclimation to cold or warm (34°C) temperatures were partially explained by variation in fiber type composition in the swimming muscle. Cold acclimation changed the abundance of 3,452 of 19,712 unique and unambiguously identified transcripts detected in the fast muscle using RNA-Seq. Principal components analysis differentiated the general transcriptional responses to cold of the 27°C and 32°C T E groups. Differences in expression were observed for individual genes involved in energy metabolism, angiogenesis, cell stress, muscle contraction and remodeling, and apoptosis. Therefore, thermal acclimation capacity is not fixed and can be modified by temperature during early development. Developmental plasticity may thus help some ectothermic organisms cope with the more variable temperatures that are expected under future climate-change scenarios.environmental physiology | fish | muscle transcriptome | functional genomics | high-throughput sequencing T emperature has profound effects on the physical and chemical processes that dictate how biological systems function. Ectothermic organisms-those that cannot regulate body temperature using endogenous heat production-are particularly susceptible to changes in environmental temperature. Species and populations can typically survive and perform across a finite range of temperatures, the breadth of which is a critical determinant of their distribution and abundance (1, 2). The physiological and molecular mechanisms underlying how ectotherms perform when faced with daily and seasonal temperature variation have attracted significant attention for decades, and this interest has intensified in an attempt to understand the potential ecological impacts of global climate change (3, 4). It is clear that temperature acclimatization can shift thermal optima and performance breadth (5), which may increase fitness and improve the viability of populations during warming (6-8). However, much of what we know about the integrative mechanisms for this ability comes from studies of juvenile and adult animals. There has been relatively little emphasis on how interactions between temperature and ...