The relationship between the actual anatomy of silicified plants and the nature of their permineralization has yet to be fully understood from a mineralogical point of view. Thin sections of silicified trunks obtained from the extinct Permo-Carboniferous arborescent plant taxa Arthropitys GOEPP., Psaronius COTTA and Dadoxylon ENDL., were studied by transmitted normal light (PPL), polarized-light (XPL), hot or scanning cathodoluminescence (CL), and electron microscopy (SEM) with energy and wavelength dispersive X-ray analysis (EDS and WDS). X-ray diffraction analysis (XRD) indicates that the SiO2 phase is highly crystalline, probably due to its extreme age (approximately 300 million years). The cathodoluminescence of the silicifed trunks is seen to be unique and related to the petrographical characteristics of SiO2 matter, which is closely connected to variation in plant anatomy. Microquartz (up to 20 μm) and fine megaquartz crystals (20–50 μm) generally produced red CL. They are present in most of the former plant tissues, especially in parenchyma and sclerenchyma, and also in cell walls and lumina of tracheids and rays of the secondary xylem. They almost completely reflect the original anatomical structures and as polyblastic textures preserve them best. Thick-walled sclerenchyma cells are usually best preserved, tracheids with lignin thickenings to a lesser extent. In contrast, megaquartz (above 50 μm) with brownish-red CL, spherulitic chalcedony with pinkish-purple or light violet CL, and agate-like structures sometimes crystallized as hyperblastic textures irrespective of the original plant tissues. This occurred especially in former thin-walled parenchyma, aerenchyma, voids, and in empty spaces and cracks. Parenchyma is thus well preserved only occasionally but aerenchyma is always transformed to an undifferentiated mineral phase. In the SiO2 ground-mass, stable red CL prevails and blue CL is less common. CL sometimes allows visualisation of important fine scale anatomical detail that is not obvious under normal transmitted light. Furthermore, in several cases short-lived blue CL was recorded, which revealed a secondary overprint caused by a later silicification phase. CL also revealed traces of earlier calcification (orange CL). Detrital mineral grains, trapped in a compact silicified body (easily exposed by CL and analyzed by SEM/EDS) can serve as a clue to plant taphonomy, as for example black sands in “mineral pockets” probably indicate well-sorted sedimentary units from original riparian environments.