The palaeoecology and palaeoenvironment of a dense cluster of regular echinoid spines that occur in an oyster-rich limestone layer are interpreted based on detailed taphonomic study. The paucispecific macrobenthic assemblage associated with these echinoid spines have been studied in the middle Miocene Geniefa Formation, Gebel Gharra, Cairo-Suez District of Egypt. Both echinoid spines and macrobenthic assemblages are dominated by moderately to well-preserved, moderately packed, highly disarticulated, moderately to poorly sorted, re-oriented, and moderately to highly fragmented specimens, confirming parautochthonous nature of this assemblage. The spines are commonly encrusted and bored. At least four taxonomic groups of encrusters are identified, including juvenile oysters, sheet-like cheilostome bryozoans, serpulids, and balanoid barnacles. The diversity of bioerosional ichnotaxa is moderate and includes Gastrochaenolites, Entobia, Maeandropolydora, Trypanites, and Spirolites. Moreover, some echinoid spines display distinct biting traces of fish, representing the first recorded of fish tooth bite marks on remains of regular echinoid spines from the Miocene deposits of Egypt. The faunal composition and trophic structure of the studied faunal assemblage indicate fully oxygenated and euhaline shallow-marine environment with meso- to eutrophic productivity level. The controlling environmental parameters include substrate consistency, bathymetry, water energy, surface-water productivity, and rate of sedimentation. Furthermore, two scenarios for sclerobionts colonisation and development of fish bite marks have been proposed. In the first syn vivo scenario, predatory fish either focused on the encrusting organisms attached to the spines or attacked the echinoid as a food source, resulting in the separation of spines from their original test during the echinoid’s life. In the second post-mortem scenario, disarticulated spines serve as a hard substrate for the colonisation of sclerobionts. Once again, the spines became subject to attacks by fish that fed on the encrusters, resulting in additional bite marks.