AimsThe study aimed to serotype the Salmonella isolates recovered from chicken and egg production chains, and to investigate the disinfectant resistance phenotypes and genotypes of these isolates. Methods and ResultsThe Salmonella isolates were serotyped, and the minimal inhibitory concentrations (MICs) of disinfectants were determined. Results showed that the Salmonella isolates recovered from both chains were diverse, and the serotypes in each part of the production chain and between the two production chains were significantly different. In the chicken production chain, 19 different serotypes were recovered, while only five serotypes were found in the egg production chain. The isolates showed a high susceptibility to didecyldimethylammonium bromide (DDAB) but a low susceptibility to benzalkonium chloride (BC), benzalkonium bromide (BAB) and chlorhexidine (CHX). Salmonella Enteritidis and Salmonella Typhimurium were more resistant to BC and BAB. The qacE1 and qacF resistance genes were detected in 267 and 77% of the isolates respectively. The qacE1 gene was frequently found in Salmonella Derby and Salm.Enteritidis (P<005). ConclusionOur findings indicated that Salmonella was commonly present in both chains, and could serve as a critical vector in spreading disinfectant resistance associated with different serotypes. Significance and Impact of the StudyThis study first demonstrated disinfectant resistance phenotypes and genotypes of serotyped Salmonella. The study highlights the need for monitoring the disinfectant resistance varied in different Salmonella serotypes.