Unicellular organic-walled microfossils from the Cambrian–Ordovician transition in Estonia (ca. 490–480 million years ago) exhibit rare characters reflecting their function as reproductive algal cysts. The studied assemblages record the evolutionary history of phytoplankton in the early Palaeozoic Era: novel morphologies appearing through the Cambrian and subsequently diversifying in the Ordovician. Well-preserved specimens were extracted following a standard palynological method and studied by light-transmitted microscopy. The galeate plexus acritarchs Caldariola, Priscogalea and Stelliferidium have revealed exceptionally preserved morphological elements and a rare structure among both fossil and extant protists – an opening with operculum (lid) in reproductive cysts, in addition to lavish vesicle ornamentation and sculpture. Analogous morphology is observed in the living dasycladalean alga Acetabularia (Chlorophyta), which possesses an intrinsic lid-forming apparatus used during the organism’s reproductive stage. Based on the observations on the fossil material and studies on the Acetabularia lid formation, we propose a model of operculum formation in the galeate plexus micro-organisms. Due to strong morphological and ecological similarities between galeate fossils and dasycladalean cysts, and the antiquity of this algal order, galeates may be positioned within green algae, more specifically Dasycladales. The unique morphology of the operculum-bearing microbiota would have required a high degree of intracellular complexity for its development, suggesting that advanced intracellular machinery was present already in the early Palaeozoic phytoplankton. Additionally, the minute prasinophyte microfossil Reticella corrugata is reported for the first time in the Upper Cambrian strata.