Stress response is important to living organisms. Identification of differentially expressed genes (DEG) and regulated pathways in response to stressors is critical to understanding the mechanisms underlying stress response. Although some progress in these fields has been obtained, there is a limited understanding of the genome-wide response to stress in fish. Moreover, the fish intestine is one of the major organs interacting with environment. However, transcriptome in fish intestine has been poorly explored. Pathogen infection, lack of feeds and salinity changes are important stressors for fish. They usually cause quite different biotic and abiotic stress response phenotypes. Therefore, we hypothesized that at the transcriptome level, the responses of intestine to these stressors are also different. In order to test this hypothesis, we challenged Asian seabass with lipopolysaccharide (LPS), Vibrio harveyi infection, fasting and high sanity, and conducted RNA-seq based on Roche/454 sequencing and bioinformatic analyses for genome-wide transcriptome in the intestine. Over one million sequence reads with an average length of 516 bp were obtained. We assembled and annotated the reads, and identified differentially expressed transcripts and regulated pathways in response to different stressors. Our data suggest that a global coordination and fine-tuning of gene regulation during different stresses. This study enhances our understanding of the mechanisms underlying the adaptive stress responses and accelerates the space of gene discovery during stress in fish.