Linezolid is one of the last-resort antimicrobials to treat vancomycin-resistant Enterococcus (VRE), a global emerging nosocomial pathogen. Worryingly, linezolid resistant VRE have been reported not long after its clinical use, mainly through mutations on the 23S ribosomal RNA genes which form the binding site for this drug. In recent years, major focus has shifted to examining the role of linezolid resistance (LR) genes including cfr, optrA and poxtA, largely due to the potential of these genes to disseminate horizontally on mobile genetic elements such as plasmids. This study was carried out to investigate rates of LR and to unravel the genetic mechanisms that underpin LR in clinical Enterococcus faecium and Enterococcus faecalis isolates obtained from healthcare facilities across Victoria from 2015-2022. We undertook comparative genomics on sequences belonging to the two pathogens to identify genes and mutations associated with LR and determined relationship with phylogenetic structure of the isolates. Across the two species we found that only a small percentage of isolates were phenotypically LR. Genetic mechanisms underpinning LR was optrA gene in E. faecalis, with multiple variants of optrA found. LR-E. faecium displayed a more diverse resistance mechanism with more than one type of linezolid resistance gene detected including cfr, cfr(B), cfr(D), optrA and poxtA, and the G2576T mutation. We also observe co-carriage of different LR genes (cfr/optrA and optrA/poxtA) among E. faecium isolates. Understanding the current trends and genomic epidemiology of LR is crucial to prevent the dissemination of resistant clones and forms an essential part for regional public health surveillance.