As Salmonella enterica serovar Pullorum remains a major economic problem for the poultry industries of countries with no efficient control measures, we presented a multidrug resistance strain S06004 (isolated from a clinically sick chicken in China in 2006) for genome sequencing. The genome comparison showed that the strain contained two prophages, the ST104 and prophage-4 (Fels2) of E. coli LF82, which were not detected in the only published genomes of S. Pullorum RKS5078 and CDC1983-67. In addition, the GyrA Ser83 point mutation, drugresistant genes, and many antibiotic pump systems that are present in S06004 may be contributing to the multidrug resistance of this strain.