Fourteen samples of the Valga-10 drill core, south Estonia, from the lower Jelgava Formation (middle Pirgu Regional Stage, Upper Katian) to the lowermost Õhne Formation (lowermost Juuru Regional Stage, Lower Rhuddanian) were investigated for acritarchs. The section is biostratigraphically and chemostratigraphically well constrained; it comprises the rugata, taugourdeaui and scabra chitinozoan zones, the ordovicicus and giradeauensis conodont zones and the Hirnantian Isotopic Carbon Excursion (HICE). The good preservation allowed the identification of three prasinophyte phycomata and 52 acritarch species including the four new species Evittia porkuniensis, Helosphaeridium tongiorgii, Nexosarium leherissei and ?Veryhachium bulliferum. One new combination is proposed: Poikilofusa obliquipunctata (Uutela & Tynni 1991) comb. nov. Comparison with contemporaneaous palynofloras shows that eastern Laurentia and Baltica share a high number of species during the latest Katian–Hirnantian. Some of these species show a potential for future improvement of biostratigraphical correlation between the uppermost Katian–Hirnantian strata of low to mid-latitude carbonate platforms in eastern Laurentia and Baltica. Conversely, significant taxonomic differences exist between the assemblage studied and typical Gondwanan palynofloras. These results suggest that the Laurentian/Baltic and Gonwanan phytoplanktonic palaeoprovinces existed during latest Ordovician times. Published data reveal similar distribution pattern for chitinozoans and graptolites during the Hirnantian. A bathymetric ridge rise associated with the opening of the Rheic Ocean, coupled with the Hirnantian glacially-driven sea-level fall might have prevented water mass exchange and mixing/migration of phytoplankton between Gondwana and Laurentia/Baltica, thus being at the origin of the observed acritarch bioprovincialism. Additionally, distribution and diversity patterns of acritarchs are compared to those of other microfossils in the Valga-10 section. Near the base of the Hirnantian (Porkuni Regional Stage), benthic organisms (ostracods and scolecodonts) and phytoplankton (acritarchs) show increasing diversity with appearances of new taxa and new morphologies. Planktonic (chitinozoans) and nektonic (conodonts) organisms show a different pattern, with a decline in diversity during the earliest Hirnantian and a marked increase in the later part of the stage. Two alternative hyptotheses are proposed to explain these differences in diversification patterns: (1) the development of a shallower, proximal environment in the locality studied during the Hirnantian glaciation may have been more favourable to the diversification of benthonic organisms; (2) the planktonic and nektonic organisms suffered the effects of glaciation more than benthonic ones.