The overall goal of this research was to advance the understanding of Salmonella and E. coli in the egg industry in Western Australia (WA). The first objective of this study was to assess the prevalence, serotype diversity, and genomic characterization of Salmonella in the egg chain (retail and farm environment) in WA. The second objective was to have a better insight on antimicrobial resistance and genomic characterization of E. coli in retail eggs. Salmonella was detected in 11.5% (23/200) of collected retail egg samples (one sample = a dozen of eggs) and 35% (93/265) of the environmental samples collected from layer farms. Salmonella Typhimurium and Salmonella Infantis were the most prevalent serovars in both farm and retail investigations. All Salmonella isolated from retail table eggs were susceptible to a panel of 14 antimicrobials, with only two isolates were found to be resistant to ampicillin. Whole genome comparative analysis of retail isolates indicated an association between Salmonella genomic variation and the management system used to raise poultry for egg production. The highest frequencies of non-susceptibility among selected generic E. coli isolated from retail eggs were observed against tetracycline (49%) and ampicillin (36%). We also reported the first detection of non-wild-type E. coli isolates against fluoroquinolones (ciprofloxacin) in supermarket eggs in Australia.