Helicobacter sud-cetorum, was cultured from the various location of the main and pylorus stomachs of a wild, stranded spotted dolphins (Stenella attenuata). High quality draft genomes of 5 isolates (2 from the main and 3 from the pylorus stomach) were sequenced using illumina MiSeq platform. Similar to H. pylori, the GC content of the genome is about 40%. The 1 million 150 bp paired end reads were denovo assembled into 27 contigs by CLC genomic benchwork and the genome size was estimated to be 1.4 mbp. Due to the high nucleotide diversity, only 15% of the reads were mapped to the two published H. cetorum strains (strain 00-7128 and 99-5656) and to two H. pylori strains (strain 26695 and J99). At least 1400 genes were annotated by Rapid Annotation using Subsystem Technology (RAST). This H. sud-cetorum strain were shown presence of the vacA gene; presence of two divergent ureAB genes (one in a urease cluster with all the accessory genes and one locating elsewhere); absence of tlpABC chemotaxis genes; and absence of cagPAI. Nucleotide-level pair-wise comparison of the flagella system between the H. sud-cetorum (strain ATFT1), two H. cetorum (strain 00-7128 and 99-5656), and five H. pylori (strain 26695, J99, G27, P12, and Puno120) suggested that they were conserved. The basal body genes were about 80% similar across the strains; the hook genes were about 70% similar; the biosynthetic and regulatory genes were about 77% similar; and the filament genes were about 60% similar. This study discuss the micro-evolution between the 5 isolates cultured from different location of the stomach and for the first time described the unique features of H. sud-cetorum genome.