Chitinozoans are a group of biostratigraphically valuable microfossils which appeared in the Tremadocian and diversified during the rest of the Great Ordovician Biodiversification Event, to become extinct in the Devonian. The early diversification of chitinozoans on the Baltica palaeocontinent has remained poorly known due to preservation and collecting bias. In this study we document the distribution of chitinozoans through the upper Tremadocian to lower Darriwilian strata in the Jägala waterfall section from northern Estonia, in order to better understand the regional diversity patterns and biogeographic links. Fifty samples were studied from the 7.5 m succession of sandstones, marls and carbonates revealing 47 chitinozoan species and 11 genera. The lowermost productive samples, attributed to the late Tremadocian, represent the earliest rich chitinozoan fauna from Baltica. Combined with previous reports this shows a diversity peak in the Tremadocian with balanced total diversity reaching 17, possibly followed by a decline in the Floian and then a rather gradual increase through the Dapingian and early Darriwilian. The new diversity curve shows more than three times higher values for the Tremadocian and Dapingian than indicated in previous studies, and thus less abrupt radiation in the Darriwilian. The Jägala section provided also new data on the regional biozonal species Conochitina cucumis and Cyathochitina regnelli, which characterize the middle and upper Volkhov and lower Kunda regional stages, respectively. Several other biostratigraphically significant taxa typical of other regions were recovered from the Jägala section, including Conochitina decipiens and Desmochitina bulla. A new short-ranging species Laufeldochitina toilaensis sp. nov. is introduced, having potential to become an index species for middle Dapingian strata. The early Darriwilian assemblage from Jägala includes Rhabdochitina sp. A with up to 2.7 mm long vesicle, making it the largest chitinozoan ever reported. •Rich assemblage of Early and Middle Ordovician chitinozoans recovered from Baltica.•A peak in regional diversity of chitinozoans occurred in the late Tremadocian.•The main phase of GOBE was more gradual on Baltica than previously known.•The largest chitinozoan with 2.7 mm long vesicle recovered from the Darriwilian.