In the long history of symbiosis research, most studies focused mainly on organelles or bacteria within multicellular hosts. The single-celled protists receive little attention despite harboring an immense diversity of symbiotic associations with bacteria and archaea. One subgroup of the ciliate
Euplotes
species is strictly dependent on essential symbionts for survival and has emerged as a valuable model for understanding symbiont replacements and recent symbioses. However, almost all of our knowledge about the evolution and functions of
Euplotes
symbioses comes from the
Euplotes
–
Polynucleobacter
system. In this article, we report a novel essential symbiont, which also has very close free-living relatives. Genome analysis indicated that it is a recently established endosymbiont undergoing genome erosion and relies on the
Euplotes
host for many essential molecules. Our results provide support for the notion that essential symbionts of the ciliate
Euplotes
evolve from free-living progenitors in the natural water environment.