The Lower and Upper Kellwasser horizons represent two anoxic events that mark the mass extinction at the Frasnian-Famennian (F-F) boundary. Among other groups, conodont animals were severely affected, but the genus Palmatolepis survived with a complete turnover at the F-F boundary. Here the fine morphological variations of the genus Palmatolepis and the sea-surface temperature evolution are quantified in two F-F boundary sections using morphometrics and oxygen isotopic composition of apatite, respectively. In accordance with other F-F sections, the isotope records show two positive excursions of ~1‰ during the Lower and Upper Kellwasser anoxic events. The conodont shape and the oxygen isotopic composition of the genus Palmatolepis are significantly correlated within the Frasnian and Famennian Stages, suggesting a strong environmental influence on the morphology of the feeding apparatus of the conodont animal. We propose that the morphological differences are linked to changes in the trophic position of Palmatolepis: enhanced organic carbon burial, which is supported by global positive carbon isotope excursions in inorganic and organic carbon during both the Lower and Upper Kellwasser events altered the primary biomass production and thus, the subsequent nutrient supply to higher trophic levels. While the carbon and oxygen isotopic shifts are of similar amplitude during Lower and Upper Kellwasser events, the variation of the shape of Palmatolepis during the Upper Kellwasser, i.e., the F-F boundary, is more pronounced than during the Lower Kellwasser.