We report here the genome sequence of Salmonella enterica subsp. enterica serovar Enteritidis MS 501, a potential human pathogen isolated from red lettuce (Lactuca sativa var. capitata) in Karlsruhe, Germany. The assembled genome size was 4,700,322 bp. A total of 4,560 coding genes, 16 rRNAs, 78 tRNAs, and 15 noncoding RNAs were predicted.