Before the onset of the Neoproterozoic Snowball Earth glaciations, eukaryotes had begun diversifying, and in their aftermath, macroscopic life, including both animals and macroalgae, became abundant and widespread. Although glacially driven mass extinctions have been hypothesized, little is known about the biosphere during and between these glaciations. Here we present new data from organic-walled microfossil assemblages from five successions in Australia and Svalbard that collectively span the first (Sturtian) glaciation and interglacial interval and integrate them with data derived from a critical evaluation of the literature to produce a new estimate of eukaryotic diversity from 850 to 650 Ma. These new glacial and interglacial assemblages consist of only smooth-walled spheroids (leiosphaerids), aggregates of cells, and filaments, in contrast to the much more diverse organic-walled microfossil assemblages found in early Neoproterozoic rocks. This contrast is not attributed to biases in deposition or preservation, but is instead interpreted as reflecting an interval of lowered eukaryotic diversity that spanned the glaciations and that may have begun millions of years prior to their onset.