The emergence of antimicrobial resistance bacteria in both the medical and agricultural fields has become a serious problem worldwide. The use of antimicrobial agents in animals for prophylaxis and growth promotion favors the selection of antimicrobial resistance in bacteria. These resistant bacteria may subsequently transmit to humans through food chain or human-animal interactions. The objectives of this study were to characterize and determine the molecular mechanisms of antimicrobial resistance in Salmonella and Escherichia coli. E. coli isolates recovered from diseased piglets and chicken in China were characterized for the antimicrobial resistance phenotype and the presence of mutation in their gyrA, gyrB, parC and parE genes. Results indicated that multiple- antimicrobial-resistant E. coli, including fluoroquinolone-resistant variants, are commonly present among diseased swine and chickens in China. DNA sequencing revealed that double gyrA mutations coupled with parC mutation conferred high-level resistance to fluoroquinolones. In addition, Salmonella isolates recovered from retail meats in the United States and China were characterized for antimicrobial resistance genotypes and the horizontal transfer of resistance determinants. The antimicrobial resistance genotypes of Salmonella were consistent to their phenotypes. Genes conferring antimicrobial resistance in Salmonella are often carried on integrons and plasmids, and could be transmitted through conjugation. To rapidly screen for the antimicrobial-resistant and virulence genes from bacteria, a DNA microarray was developed to analyze the antimicrobial resistance and virulence genes from Salmonella and E. coli. Results indicated that microarrray was an effective method to rapidly screen antimicrobial resistance and virulence genes in Salmonella and E coli. Finally, molecular mechanisms of fluoroquinolone resistance, including over-expression of efflux pumps and target gene mutations, were characterized among laboratory-induced and field-acquired fluoroquinolone-resistant Salmonella. The efflux pumps which were overexpressed in resistant strains were deleted and mutated gyrA and parC genes were replaced to determine the contribution of efflux pump and target gene mutations in fluoroquinolone-resistant Salmonella. When Salmonella are exposed to fluoroquinolone, certain efflux pumps are overexpressed in tandem with particular mutations in topoisomerase genes (gyrA and parC). Based on deletion mutagenesis studies, it appears that the most relevant genes with regards to the selection of fluoroquinolone resistance phenotypes among Salmonella are the AcrAB-tolC efflux pump and the gyrA portion of DNA gyrase gene.