Based on whole genome sequence analysis, the antibiotic resistance genes and virulence genes in Salmonella typhimurium, which was isolated from fecal samples of children under 5-year old, were investigated and their resistance mechanisms were tested.Methods The antimicrobial susceptibility of 321 Salmonella typhimurium strains isolated from fecal samples of diarrheal children under 5-year old was tested by broth microdilution method as the Clinical and Laboratory Standards Institute recommended.Then, Salmonella typhimurium strains S1, S2 and S3with different resistance phenotypes (S1:susceptible to all 12 tested antibiotics; S2:resistant to tetracycline only; S3:resistant to 10 antibiotics except imipenem and meropenem) were selected for whole genome sequences using Illumina Hiseq 2000. The antibiotic resistance genes and virulence genes were annotated with antibiotic resistance genes database (ARDB) and virulence factors of pathogenic bacteria database (VFDB). Comparing to Salmonella typhimurium str. LT2, the genetic mutation analysis of gyrA, gyrB, parC, and parE in the 3 tested strains was performed by GENtle software. Results All 321 Salmonella typhimurium isolates were susceptible to imipenem and meropenem, while 271 (84.4%, 271/321) and 269 (83.8%, 269/321) strains were resistant to tetracycline and ampicillin, respectively. Besides, 206 (64.2%, 206/321) showed multiple drug resistance, and 11 (3.4%, 11/321) strains were ESBLs-producing strains. The sizes of genome of S1, S2 and S3 were 4 876 427 bp (GC content:52.18%), 4 970 690 bp (GC content:52.14%)and 5 133 380 bp (GC content:51.87%), respectively. Furthermore, the ARDB annotation results showed that 18 out of 4 825 genes of S1,0 out of 4 936 genes of S2, and 32 out of 5 082 genes of S3 were associated with antibiotic resistance, respectively. In detail, tetA and sul2 genes were annotated in S2. While sul1/2/3, tetB, AAC(3)-IV, AAC(6′)-I, ANT(2″)-I, ANT(3″)-I, aphA1, blaCTX-M-14, blaOXA-1, catB3, cml_e1 and cml_e3 were annotated in S3. Compared with Salmonella enterica subsp. enterica serovar typhimurium str. LT2, the 87^th cod on of gyrA in S3 changed from GAC to AAC (Asp87→Asn). Meanwhile, the VFDB annotation results showed that 130 out of 4 825 genes of S1,9 out of 4 936 genes of S2, and 120 out of 5 082 genes of S3 were associated with virulence, and the major types of virulence were type three secretion system and adherence factors.Conclusion The antibiotic resistance of Salmonella typhimurium isolated from fecal samples of children under 5-year old was very serious. The resistance genes obtained by genome annotation were in good accordance with resistance phenotypes. Moreover, various virulence genes were annotated in this study. There sultscouldshed light on drug resistance mechanisms and pathogenicity of Salmonella typhimurium isolates, health risk assessment, and finally preventing and controlling the contamination of Salmonella typhimurium isolates.