We report, here, the first proteomics study of a grouper embryonic cell line (GEC) infected by Singapore grouper iridovirus (SGIV). The differential proteomes of GEC with and without viral infection were studied and quantified with iTRAQ labelling followed by liquid chromatography/tandem mass spectrometry (LC-MS/MS). Forty-nine viral proteins were recognized, of which 11 were identified for the first time. Moreover, 743 host proteins were revealed and classified into 218 unique protein groups. Fourteen host proteins were upregulated and five host proteins were downregulated upon viral infection. The iTRAQ analysis of SGIV infection in GEC provides an insight to viral and host gene products at the protein level. This should facilitate further study and the understanding of virus-host interactions, molecular mechanisms of viral infection and pathogenesis.