Abstract: Gibel carp (Carassius auratus gibelio) infected with Cyprinid herpesvirus 2 (CyHV-2), damaged many organs including intestinal mucosa. Total RNA of intestinal mucosa from CyHV-2 diseased and normal gibel carp were extracted for RNA-Seq. Transcriptome assembly from RNA-Seq data without a reference genome was conducted by Trinity (version: v2012-10-05, min_kmer_cov 2) software. Single gene is annotated by using different databases. Software and the database of the functional gene annotation are SwissProt (NCBI blast 2.2.27+, Blast2GO v2.5), KOG (NCBI blast 2.2.27+), PFAM (HMMER 3.0 package), KEGG (KOBAS, NCBI blast 2.2.27+). Gene expression was analyzed by edgeR package. 3335 up-regulated genes and 4435 down-regulated genes were observed, indicating a significant injury in the intestinal mucosa by CyHV-2 infection. The metabolic disorder for enterohepatic circulation of bile acids was supported by the reduced gene expression that regulate cholesterol and bile acid synthesis metabolism and other physiological processes, secretion, absorption and transportation. As a consequence, CyHV-2 infection in Crucian carp decreased the serum bile acid content by 99% and cholesterol content by 10%.