The greatest ice ages in Earth’s history occurred during the 654–635 Ma Marinoan glaciation, when glaciers reached tropical oceans and our planet approached a snowball Earth condition. Paleontological and genomic data suggest that several eukaryotic groups must have survived the Marinoan glaciation. But their fossil record is scarce and limited to microbes, whose ecological and physiological ranges are poorly constrained, thus hampering a full understanding of how and where eukaryotic life—particularly macroscopic phototrophs—survived this snowball Earth. Here we report carbonaceous compression fossils from the Marinoan-age Nantuo Formation in South China. These fossils are preserved in thin black shales sandwiched between glacial diamictites deposited in inner shelf environments of the mid-latitudinal Yangtze block. Some of these fossils are interpreted as benthic macroalgae. Thus, the Marinoan glaciation must have been punctuated by episodes of open waters where habitable benthic substrates were available in the photic zone and along the coast of mid-latitudinal continents. Such open waters may have been the refugia where macroscopic phototrophs survived the Marinoan glaciation and subsequently diversified in the early Ediacaran Period.