The Middle and Upper Ordovician rocks of Baltoscandia have been divided into spatially distinct, composite litho- and biofacies units called confacies belts. The precise regional correlation of outcrops and boreholes, which is necessary for biodiversity analyses, has always been problematic due to the pronounced biogeographical differentiation of macrofossils and horizontal lithofacies changes. We used a computer-assisted numerical sequencing program (CONOP9) to construct a correlation model and composite range chart from the stratigraphic range data of 159 conodont species in 24 boreholes and outcrops in Baltoscandia. We converted the composite section into a timescale in which to calculate the biodiversity, extinction, origination and fossil sampling probabilities through the Ordovician Period. Rates of extinction and origination were calculated using both simple approaches which do not incorporate estimates of sampling probability, and also more complex maximum-likelihood approaches based on Capture–Mark–Recapture (CMR) models. Our data show that overall biodiversity increases steadily from the base of the Paltodusdeltifer Zone to the uppermost Baltoniodusnorrlandicus Zone and then maintains an uneven diversity plateau until the earliest Sandbian. Diversity then declines dramatically throughout the remainder of the Ordovician. CMR analyses suggest that extinction rates remain constant throughout most of the Ordovician indicating that the dramatic late Middle and Late Ordovician decline in conodont diversity in Baltoscandia is attributable to depressed origination.