We identified an alphaproteobacterium in the digestive gland of the abalone species Haliotis discus hannai. This phylotype dominated our 16S rRNA clone libraries from the digestive gland of H. discus hannai. Diversity surveys revealed that this phylotype was associated with H. discus hannai and also in another host species, H. gigantea. Whole genome phylogenies placed this bacterium as a new member affiliated with the family Rhodospirillaceae in Alphaproteobacteria. Gene annotation revealed a nearly complete glycolysis pathway but no TCA cycle, but the presence of anaerobic ribonucleoside-triphosphate reductase and oxygen-insensitive NAD(P)H-dependent nitroreductase, which show the genomic potential for anaerobic metabolism. A large cluster of genes encoding ankyrin repeat proteins (ANK) of eukaryotic-like repeat domains and a large gene set for the flagellar system were also detected. Alginate-binding periplasmic proteins and key genes responsible for alginate assimilation were found in the genome, which could potentially contribute to the breakdown of the host's alginate-rich macroalgal diet. These results raise the possibility that this novel alphaproteobacterium is a widespread member of the abalone microbiome that may use polysaccharides derived from its host's macroalgal diet.