A bed by bed analysis of the Bonarelli Level (late Cenomanian) in the Bottaccione Gorge and the Contessa Valley (Gubbio, Italy, area) reveals ichnofabric variations that follow lithofacies changes. Ichnofabric analysis has been approached in ~60 samples for every section, using thin sections of rocks and wet cut surfaces for three-dimensional observations. The ichnofabric includes five ichnotaxa: Chondrites isp., Planolites isp., Thalassinoides isp., Trichichnus linearis, and Zoophycos isp.; their abundance and preservation fluctuate with the substrate consistency, oxygen content, and productivity. The ichnotaxa are absent in many beds that show primary lamination and were deposited under true anoxic conditions, but it is surprising that they are present in many thin beds inside the Bonarelli interval (10 in Bottaccione and 14 in Contessa). In the underlying and overlying Scaglia Bianca (late Cenomanian) carbonate deposits, the presence of a totally bioturbated background, together with superimposed discrete trace fossils (the same ichnotaxa as in the Bonarelli Level), reveals the absence of anoxic conditions (except for cherty layers), but the presence of minor fluctuations between aerobic and slightly dysaerobic conditions is marked by changes in ichnotaxa abundance.