Taphonomic features of 156 graphoglyptids and other trace fossils preserved as hypichnia of thin-bedded turbidites in Oligo-Miocene flysch of the northern Apennines (central Italy) were analyzed. Two biogenic taphonomic categories—deformation and elongation—were produced in hemipelagic mud by the behavior of endobenthic organisms. Deformation includes such features typical of bulldozing and burrowing as twisting, squeezing, tilting, thickening, and widening. Elongation is considered a primary biogenic character controlled directly by the tracemaker. Taphonomic features induced by such physical agents as currents and creep usually developed unidirectionally and include stretching, straightening, smoothing, bending, tapering, thickening, and thinning. These features, associated with hundreds of microgrooves (5–10 per 0.01 m2) interpreted as mud-current lineations, suggest that currents were active and produced deformational structures of fluting before, during, and after the biogenic activity. Preservation of such delicate structures recognizable at different levels is particularly noticeable when a thin layer of fine material settled by suspension, molding all structures and producing a cemented film. Deformational structures may be particularly well preserved in thin-bedded (3–6-cm-thick) and fine-grained calcarenitic turbidites as in diluted turbulent flow deposits that fringed the isolated Verghereto High. Activities of epi- and infaunal communities in this area are also exceptionally well preserved. Physical taphocharacters of graphoglyptids are interpreted in two ways: (1) as true tool marks produced in mud by a tractive water mass preceding sand deposition by turbidite flows, or (2) as structures inherited from preturbidite phases. Taphonomic analysis in deep-sea deposits, therefore, is a promising methodology to resolve the preservational state of trace fossils above and below the soles of turbidites.