Quorum-sensing (QS) signaling molecules are able to mediate specific gene expression inside spoilage bacteria in response to population density and thus are implicated in food spoilage. In the present work, a total of 102 strains of spoilage bacteria were isolated from Pseudosciaena crocea at 4 °C storage, and of these, 60 strains were identified as Shewanella spp., and 48 strains (47.1%) were identified as S. baltica. In addition, the spoilage capabilities of three different S. baltica strains (00A, 00B, and 00C) were compared by total volatile base nitrogen (TVB-N) and sensory analysis (off-odors). Furthermore, four cyclic dipeptides (diketopiperazines, DKPs) that function as QS signal molecules were isolated and characterized from the extracellular metabolites of S. baltica 00C which had the strongest spoilage activity based on gas chromatography mass spectrometry (GC-MS). By supplementation of four synthesized DKPs, the spoilage capability of S. baltica could be significantly enhanced. So far, this was the first attempt to characterize DKPs as the signaling molecules in QS of S. baltica. Our study may provide some evidence of the role of DKPs involved in microbial spoilage.