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Bacterial foodborne pathogens are significant public health and economic burdens. Whole-genome sequencing (WGS) offers unprecedented power to characterise the molecular epidemiology of both epidemic and emerging foodborne pathogens. The objectives of this thesis were to elucidate the genomic epidemiology of an epidemic foodborne pathogen Salmonella enterica serovar Enteritidis and an emerging foodborne pathogen Escherichia albertii, and to develop a multilevel genome typing (MGT) scheme and database for genomic surveillance of S. Enteritidis. S. Enteritidis is a global epidemic foodborne pathogen. Multi-country outbreaks and multidrug resistance (MDR) are of increasing concern. In this thesis, the core genome of S. Enteritidis was defined and used to develop a global publicly available MGT database for S. Enteritidis (https://mgtdb.unsw.edu.au/enteritidis/). By analysing all publicly available genomes using MGT, the global genomic epidemiological characteristics of S. Enteritidis were elucidated in detail. Further, the application of MGT was evaluated for the local public health surveillance of S. Enteritidis in Australia. The S. Enteritidis MGT database was found to be powerful in the rapid determination of the population structure, comparison of isolates from different regions, sources and time periods, investigation of international outbreak clusters, and identification of isolates related to MDR and invasive infections. E. albertii is an emerging diarrhea-causing pathogen. The genomic epidemiological characteristics of E. albertii remain unclear. This thesis analysed 169 newly sequenced E. albertii genomes from China and 312 publicly available genomes. The E. albertii population was divided into two clades and eight lineages, with 3 lineages more common in China. Virulence genes were found to be distributed differently among lineages. Seven new subtypes of the intimin encoding gene eae and one new subtype of the cytolethal distending toxin gene cdtB were identified. Alarmingly, 85.9% of the Chinese E. albertii isolates were predicted to be MDR with 35.9% harbouring genes capable of conferring resistance to 10 to 14 different drug classes. The findings in this thesis provide fundamental and new insights into the genomic epidemiology of S. Enteritidis and E. albertii. The open MGT database was shown to be a good candidate in global and local public health surveillance of foodborne pathogens.