The bituminous black pelite of the Messel UNESCO world heritage site is an exceptional palaeobiological archive from the Middle Eocene greenhouse climate. The pronounced homogeneity of the annually laminated pelite through a time interval of 640 kyr complicates the relative stratigraphic classification of fossil remains and is, thus, largely dependent on particular marker horizons within the uniform sedimentary column. We analyzed the most prominent marker horizon M using petrographic microscopy, X-ray powder diffraction, and electron probe microanalyses to identify and characterize its structure and phosphate-dominated mineralogy. Based on our analytical data, we suggest that this phosphatic marker horizon resulted from the exceptional combination of external tephra enclosed in bacteria and algae-rich layers, producing a coupled phosphorus and cation diffusion during diagenesis. Mantienneite (KMg2Al2Ti(PO4)4(OH)3 • 15H2O) is documented for the first time in the Messel fossil deposit. The diagenetic succession of messelite, montgomeryite, and mantienneite precipitation reflects the internal heterogeneities in primary mineral composition of an ash layer. Kerogen maturation and hydrocarbon migration produced acidic, reducing pore fluids with high P concentration, which enhanced the mobility of Al and Ti. The mantienneite-forming reaction marks the change from a regime of reducing to oxidizing conditions. With the deposition and diagenesis of the marker horizon M, a singular event is preserved in a sedimentary sequence otherwise regarded as largely uniform over a time span of about 640 kyr.