To study the molecular epidemiological characteristics of Salmonella enterica subsp. enterica serovar Senftenberg (Salmonella senftenberg) in Shanghai, from 2006 to 2007. A retrospective analysis in 2006 and 2007 was performed to explore the source of food-borne Salmonella senftenberg. The isolates from diarrhea patients between 2006 and 2007 were identified, including biochemical test, hilA and invA gene phenotyping, drug susceptibility, Riboprinter((R)) (RP) and pulsed-field gel electrophoresis (PFGE). Of the diarrhea patients isolates in the monitoring program on non-typhi Salmonella infection in the year of 2006 in Shanghai, number of patients caused by Salmonella senftenberg ranked the third. The stock of Salmonella senftenberg food-born isolates were derived from swine and beef products between 2003 and 2005. All of the strains from diarrhea patients were susceptible to antibiotics except tetracylina (75.6%). With RP and PFGE molecular typing, the two groups (with hydrogen sulfide and hilA, invA gene or without) could be divided into two different independent clone cluster in genetics. 34 strains of diarrhea were divided into 16 PFGE typing-pattern, and among them 12 strains including type 4 (4 strains), type 5 (1 strains), type 6 (6 strains), type 7 (1 strains) and 13 strains including type 11 (3 strains), type 17 (5 strains), type 23 (5 strains) were two different dominant clone cluster. The epidemic of Salmonella senftenberg within 2006 might have been the result of a long period of case occurrence in Shanghai. This rare outbreak belonged to a cluster of outbreaks caused by two different PFGE clone clusters. Data suggested that the genetic clone of Salmonella senftenberg might have been unstable and the source of contamination were complicated, with the characteristics as the obvious decreasing number of patients, with no food-borne isolates in 2007.