We report aerobic eukaryotic microbial life in the dimly lit anoxic water layer of a small freshwater lake. The microbial eukaryote is the ciliated protozoon Histiobalantium natans. Electron microscopy of thin sections shows that the cytoplasm of the ciliate harbours sequestered chloroplasts and sequestered mitochondria. The sequestered chloroplasts are attached or in very close proximity to the ciliate's own mitochondria. The sequestered mitochondria also seem to be associated with host-ciliate mitochondria. We suggest that the oxygenic photosynthetic activity of sequestered chloroplasts, perhaps enhanced by respiration in sequestered mitochondria, contributes to servicing the respiratory oxygen requirements of the ciliate host in its anoxic habitat. Our observations are novel, with the discovery of an aerobic microbial eukaryote capable of thriving and completing its life cycle in an anoxic environment, fuelled by oxygen generated by sequestered chloroplasts. The acknowledged flexibility and functional diversity within eukaryotic microbial communities still have many secrets to release.