We report here the near-complete genome sequence of “
Candidatus
Spirobacillus cienkowskii,” a spiral-shaped, red-pigmented uncultivated bacterial pathogen of
Daphnia
spp. The genome is 2.74 Mbp in size, has a GC content of 32.1%, and contains genes associated with bacterial motility and the production of carotenoids, which could explain the distinctive red color of hosts infected with this pathogen.