The aim of this study was to investigate sequence-based genotyping methods to distinguish 27 Riemerella anatipestifer isolates from ducklings in South Korea. The 16S rRNA sequences of the 27 R. anatipestifer isolates showed 99�100% similarities to each other and to reference sequences from Genbank (AY871822.2, AY871834.2, CP002562.1, EU715016.1, EU016548.1, EU715000.1, EU715008.1 and EU715011.1). In addition, the ompA gene sequences of 25 of the 27 R. anatipestifer isolates were 100% identical to each other, and these sequences were also 100% identical to reference sequences (CP002562.1, GQ415419.1, DQ059079, FJ765034.1, AY606207.1, AF104937.1, and FJ765033.1). Alternatively, four housekeeping genes (mdh, gdh, pgi, and rpoB) and three virulence-associated genes (prtC, hagA, and sspA) were used for a multi-locus sequence typing (MLST) and a single-locus sequence typing (SLST) among R. anatipestifer isolates. Compared to 16S rRNA and the ompA gene, seven genes showed higher genetic divergence patterns, and the isolates were separated into three distinct groups in phylogenetic trees.