Major lineages of modern eukaryotes, represented primarily by microscopic taxa, are thought to have originated during the Neoproterozoic, but microfossils older than 635 Ma rarely have unambiguous relationships to modern microscopic eukaryotes. Here we report exceptionally preserved 715–635 m.y. old eukaryotic tests in limestone strata of Mongolia. The ∼100-μm-long organic-rich three-dimensional tests have flask-like shapes, constricted necks, distinct and often thickened collars, and flexible walls composed of densely packed alveolar structures. The combined morphological and ultrastructural characters of these Cryogenian tests are remarkably similar to the tests of tintinnids, modern planktonic ciliates. Eukaryotes forming recalcitrant organic or mineral-rich tests before 635 Ma may have increased export and burial fraction of organic carbon, driving an increase in atmospheric oxygen and the subsequent radiation of metazoans.