•Two QS autoinducers were identified in the SSO, Shewanella baltica.
•The higher DKPs and AI-2 activities were found in the stronger spoiler of S. baltica.
•Regulation of cyclo-(l-Pro-l-Leu) in the spoilage potential of S. baltica was proved.
•AI-2 might not play a signaling role in the spoilage of S. baltica.
•QS promotes the competitiveness of H2S producing bacteria in the spoilage of P. crocea