Carbonate sedimentology, microfossil palaeontology and carbon isotope stratigraphy have been studied at the Triassic-Jurassic boundary in the Northern Calcareous Alps at the Fonsjoch and Schlossgraben sections in Austria. The carbonate microfacies and microfossil results of the Upper Rhaetian at Schlossgraben are in accordance with previous research indicating a deep subtidal environment within the Eiberg Basin. The so called event bed (T-Bed) is characterised by a successive diversity decrease and disappearance of ostracod taxa which was most probably caused by oxygen deficiency. Lithofacies and micropalaeontologic data from the uppermost Rhaetian at Fonsjoch are indicative of a shallow subtidal environment and existence of a nearby carbonate platform edge. Low diversity ostracod assemblages of juvenile Cytherellidae occurring above the event bed point to a second interval of suboxic conditions in the latest Rhaetian of the Eiberg Basin. For both sections, the late Rhaetian bulk carbonate carbon isotopes of about 1 parts per thousand reflect the near primary signal of the ancient seawater, and the well-known and prominent initial negative delta 13C excursion is present, starting in the limestones of the uppermost Eiberg Member and reaching a minimum within the Schattwald Beds. The delta 13Ccarb values remain low in the Schattwald Beds in both sections and this might be explained by diagenetic alteration, because it contrasts the delta 13Corg trend which returns to heavier values here. However, delta 18O versus delta 13Ccarb cross-plots for the lower beds of the Tiefengraben Member and the Schattwald Beds show only negligible correlation supporting an interpretation that at least the carbonate carbon isotope values represent near primary signals also in this stratigraphic level. Accepting this interpretation, the new results imply that the primary trends of the delta 13Ccarb and delta 13Corg are different, suggesting that the bulk organic matter sources have changed temporarily. These results further indicate that organic carbon isotope trends must be regarded with caution when used as a chemostratigraphic tool, and especially the positive carbon-isotope excursion at the Triassic-Jurassic boundary does not necessarily represent a time-correlative chemostratigraphic marker.