Streptococcus suis serotype 2 is a zoonotic Gram-positive bacterium responsible for arthritis, meningitis, pneumonia and septicemia in swine and humans. Little information about the regulation of iron on its gene expression had been reported. In this study, 63 S. suis genes upregulated under an iron-restricted condition were identified using selective capture of transcribed sequences (SCUTS) technique: 23 genes involved in metabolism, 22 genes responsible for the replication and genetic information proceeding of the bacteria, eight genes relative to the construction of the cell wall, five ATP-binding cassette transporters, four transcriptional regulators and one uncharacterized gene conserved among streptococcal species. To adapt to the stress, S. suis modulated its physiological activities, which were validated by the upregulation of RelA (a crucial enzyme in stringent response), ArcA (a component of the arginine deiminase system catalyzing the conversion of arginine to ornithine) and CpdB (a cell surface protein that is a substrate of sortase A). All of them were reported to be virulence factors in S. suis or other bacteria. Besides, together with the results of quantitative reverse transcriptase PCR, we found that several homologous genes (fur, fhuGBDA operons) associated with iron uptake as reported in other bacteria were also upregulated under an iron-restricted condition in S. suis.