Salmonella is the second causative agent of foodborne bacterial gastroenteritis in Australia, which also has the highest Salmonella notification rate in comparison to other industrialised countries. With the number of cases increasing annually, antimicrobial resistance (AMR) patterns are also emerging. Whole-genome sequencing (WGS) has paved the way for in-silico analysis providing improved genomic techniques and surveillance. The objective of this study was to determine whether WGS could replace phenotypic sensitivity testing at the Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), the national Salmonella reference laboratory. The final dataset included 3,656 Salmonella isolates that had both genotypic data obtained from WGS and phenotypic data that incorporated agar dilution sensitivities on nine clinically relevant antimicrobials interpreted using Clinical and Laboratory Standards Institute guidelines. Overall, the sensitivity and specificity rates were above 98% with 0.22% (n=67/29,785) discrepant combinations primarily due to streptomycin. AMR was observed in 831 isolates of which 473 were multidrug resistant (MDR, resistance to ≥3 antimicrobial classes) expressed by 25 serovars. Genes encoding resistance was highest against ampicillin (blaTEM-1) followed by sulphathiozole (sul2), tetracycline (tetA), streptomycin (strA-strB), cefotaxime (blaCMY-2) and chloramphenicol (floR) with an S. Kentucky ST198 and S. Indiana ST17 isolate displaying resistance to 7/9 antimicrobials. The two prevalent MDR antibiograms were resistance to ampicillin, chloramphenicol, cefotaxime, streptomycin, sulphathiozole and tetracycline (ACCfSSuT) and resistance to ASSuT, and were mainly observed in S. 4,[5],12:i:- ST34 isolates with the most common genotype being blaTEM-1, blaCTX-M-55, catA2, floR, strA-strB, sul2, tet(A) and blaTEM-1, strA-strB, sul2, tet(B), respectively. For MDR S. Enteritidis ST11 isolates, resistance to ampicillin, sulphathiozole and tetracycline with decreased ciprofloxacin susceptibility (ACpISuT) was observed in 17/39 (43.59%) isolates with blaTEM-1, sul2, tet(A) and gyrA[87:D-Y] being the most frequent genotypic pattern. In conclusion, this study demonstrated a high correlation between WGS and phenotypic sensitivity testing and highlighted that WGS can significantly improve AMR surveillance by simultaneously screening for AMR and emerging multidrug resistance patterns as compared to routine phenotypic methods.