Excellently preserved, pyritized radiolarian skeletons have been found within the Upper Cenomanian deposits in the Pieniny Klippen Belt (PKB—Carpathians, Poland). On the basis of a study of their chemical composition, structure of replacing skeletons and exceptional preservation of all morphological details, we propose a new model where the pyritization process took place not in sediment but while the radiolarian skeletons were suspended in the anoxic water column. The radiolarians rich in organic matter, sinking through the upper (iron-rich) part of an anoxic water column, became the sites of organic matter decomposition and enhanced bacterial sulphate reduction. Dissolved iron in this zone diffused into the radiolarians and precipitated as iron sulphides replacing the opaline skeletons. This process was controlled by the rates of opal dissolution and of bacterial sulphate reduction, and the availability of dissolved iron. The preservation of radiolarians in the Upper Cenomanian deposits from different depth sub-basins of the PKB was compared. We found that the extent of pyritization and preservation of radiolarian skeletons may be dependent on the depth of the basin and the position of the oxic-anoxic interface.