The genome sequences of two Thioalkalivibrio sulfidiphilus strains, SGAR-7 and SGAR-13, isolated from a pilot-scale haloalkaline biodesulfurization (BD) installation, are reported. The genomes comprise Flavocytochrome c sulfide dehydrogenase and SoxAX cytochromes, which are essential for respiration and thiosulfate oxidation, offering insights into Thioalkalivibrio’s role in BD.