From the Notes of Nikan Shrubcover, Concerning the Black Tower

Zaphon’s tower rises above the city of Ekron and even the Lunar Mounds that ring the back of the city. I can’t fathom a structure being as large as the Tree, let alone larger than it, but by most accounts the Black Tower would dwarf, not only the Tree, but even the mountains that form the valley of Burrwood. There are no records of how or when it was built and the dark volcanic stone seems completely out of place when compared to the generally sedimentary rock layers that make up most of both the Lunar Mounds and the Pillars of Heaven. It is entirely possible that Zaphon simply enslaved the local population and forced them to build the Black Tower. Another possibility is that Zaphon himself crafted the tower using his own arcane arts.