In Australia, Salmonella enterica serovar Enteritidis is the second most prevalent cause of salmonellosis. It is mainly travel-related with only a few local outbreaks reported, however, a large-scale local outbreak occurred in 2018. This study aimed to characterise the genomic features of Australian S. Enteritidis and compare them with international strains using a standardised typing method. 573 S. Enteritidis isolates from two Australian states across two consecutive years were analysed using the S. Enteritidis multilevel genome typing (MGT) scheme and database (MGTdb) - which contained 40,390 publicly available genomes from 99 countries. All Australian S. Enteritidis strains were divided into three phylogenetic clades (A, B and C) with clade A (16.4%) and clade C (3.4%) being of local origin. Clade A caused small-scale local outbreaks, clade B caused the large 2018 outbreak, and clade C caused sporadic infections. Clade B (80.1%) isolates belonged to seven previously defined lineages but were dominated by the global epidemic lineage. The sequence types (STs) of Australian isolates of this lineage showed higher similarity to that of Asia. A large eggs-associated local outbreak, which was caused by a recently defined clade B lineage common in Europe, was closely related but not directly linked to three international isolates from Europe. Additionally, antimicrobial-resistant genes were only found in Australian clade B isolates, with a predicted multidrug resistance (MDR) rate of 11.9%. Over half (55.8%) of the MDR isolates belonged to 10 MDR-associated MGT-STs; these STs are also frequently found in Asia. IncX1 plasmids were frequent in the MDR Australian isolates. Overall, this study investigated the genomic epidemiology and the first large outbreak of S. Enteritidis in Australia using MGT. The open MGT platform enables standardised and sharable nomenclature that can be effectively applied to public health agencies for unified surveillance of S. Enteritidis nationally and globally.