Abstract: To investigate the effect of temperature on transcripts and relative mRNA levels, high-throughput RNA sequencing were used for Yersinia ruckeri grown at 28℃ and 37℃. After the quality control, all differentially regulated genes were enriched and annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and verified by Rockhopper software. The results showed that 173 differentially expressed genes were identified (P-value<0.05), including 58 up-regulated genes mainly enriched in several KEGG pathways: phosphotransferase system, starch and sucrose metabolism, galactose metabolism and other glycan degradation; and 115 down-regulated genes mainly enriched in several KEGG pathways: two-component system, thiamine metabolism and flagellar assembly. In summary, the SC09 had lower motility and weaker glucose metabolism at temperature of 37℃. The compensatory overexpression of some specific carbohydrate metabolism might play important roles for the survival of this bacterial under high temperature. This study provides an important basis for further research on the molecular mechanisms of SC09 in different temperatures.