Abstract: The poor resistance of many important cultured fish species to low or high temperature brings many restrictions and difficulties to aquaculture. Since fish is more sensitive to cold or heat stress at embryo and larva stages, fish seedling breeding is often badly affected by abrupt temperature fluctuations. Although gene expression in mature tissues of several fish species exposed to temperature stress has been characterized by microarray analysis, the effects of temperature stress on gene expression in fish larvae has not been reported. In order to investigate the transcriptional response of fish to temperature stress at larval stage, the hatched zebrafish larvae at 96 hours after fertilization (hpf) were exposed to cold (16℃) or heat (34℃) stress for 12 and 24 hours respectively, and the expression of genes was detected by microarray analysis. The design of this study was aimed to identify common stress response genes regulated by both cold and heat stress and cold or heat stress specific genes. When compared to the controls maintained at 28℃, a total of 3633 genes were identified to be differentially expressed under temperature stress exposure. Cold stress regulated more genes than heat stress at both time points and the number of cold-inhibited genes was larger than that of cold-induced genes. Only a small part of these differentially expressed genes were regulated by both cold and heat stress. The results of bioinformatic analyses indicate that cold induced genes are mainly involved in biological processes including RNA processing and ribosome biogenesis; however, genes induced by heat stress are mainly associated with stress response and unfolded protein folding. Genes down-regulated by cold stress mainly participate in biological functions such as proteolysis, visual perception and iron ion binding, while heat-inhibited genes are mainly involved in biological processes including DNA replication, neurological system process and steroid biosynthesis. In addition to genes previously reported to be regulated by temperature stress, this study identified many cold- or heat-stress responsive genes, such as those involved in RNA processing, rnmtl1a (RNA methyltransferase like 1a) and pus3 (pseudouridylate synthase 3); and genes associated with transcriptional regulation, twistnb (TWIST neighbor) and aebp2 (AE binding protein 2). It could be concluded that a large number of genes and biological processes were regulated to establish the acclimated physiological status upon the exposure of fish to cold or heat stress. In-depth investigations on expression regulation and biological functions of genes specifically induced by cold or heat stress would further reveal molecular mechanisms underlying the cold or heat acclimation of fish and provide theoretical fundamentals for breeding cultured fish strains with cold- or heat-resistant ability.