We describe the characterization of Salmonella enterica serovar Typhi, isolated from the blood of patients with perforation and non-perforation typhoid fever, by a combination of conventional microbiological tests, 16S rRNA gene sequencing, and flagellin gene and CDP-tyvelose epimerase (rfbE) gene sequencing. The 16S rRNA gene sequencing showed that there were four base mutations from perforation samples and only three from non-perforation samples. These findings indicated that the isolates were a strain of Salmonella enterica. The flagellin gene sequences from the two groups were 100% identical to that of the H1-d flagellin gene of serovar Typhi. Sequences of the rfbE from both groups were also 100% identical.