One of the really risky things archaeologists do is to attempt to find reasons why people in the past did certain things. We don't really know why many civilizations of the past did things in a particular way, unless we find a court document that details motives—and even then, how do we trust that a given document accurately describes all or even part of the reasons? Can't be done.
However, I can surmise a few reasons why a conquering civilization might want to rebuild in the same exact place.
It is quite possible that the reasons that caused the original placement of a site or building are the same ones that make it attractive to the conquerors. An advantageous location might be at the mouth of a river or at a good port, such as at the Phoenician and Roman city of Cadiz in Spain. Another great location would be on an important trade roadway, such as at the Merv Oasis in Turkmenistan, located on the Silk Road and used throughout the medieval and Islamic period. Other advantageous locations might be environmental—a nice breeze, a good visibility of the region, access to a fresh water spring, reuse of existing walls or causeways. It might even be as simple a reason as it was cheaper to reuse the old foundations of a building, than to pull it down and build elsewhere.
Carthage in modern day Tunisia is a great example of an economic rebuild. At the end of the Punic Wars, the Roman senate declared that it be sacked and abandoned for all time. But within fifty years, Roman citizens were living at Carthage—the climate and advantages were just too great to ignore.
In most circumstances in the past, although a civilization has been conquered, its people are still living in the cities in which they've always resided. A conquering civilization might be interested in winning over the hearts and minds of the people, and rebuilding destroyed monuments, or tearing down old monuments and building new ones might put the stamp of possession for a particular city. Constantinople in modern-day Turkey is a great example of a city where repeated conquerors placed their stamp of possession using architecture. My personal guess is that this is one of the most compelling reasons for rebuilding on ruins; but that doesn't leave archaeological evidence or documentary evidence either.
A conquering civilization might have a radically different notion of what is acceptable religious behavior. In these circumstances, the previous religious structures must be obliterated as heretical. This kind of replacement is often evident in written records of the conquering civilizations. Examples of this kind of replacement include the Spanish cathedrals in Mexico City, placed over the ruins of Tenochtitlan, and the Taliban's destruction of the Buddhist monuments in Afghanistan (although the Taliban have been too busy to rebuild these days).
I believe it is also true that some rebuilds were completed to obliterate the presence of the predecessor civilization thus enabling a clean conscience. One example of destruction-by-guilt is the loss of Native American earthworks in the American midwest. For the first part of European settlement, people believed that the great burial and effigy mounds of the central United States had been built by a lost tribe of Israel, called the Moundbuilders. Part of the justification for American settlement was a belief that the Native American residents weren't sophisticated enough to deserve to live there. But when in the 1860s and 1870s it became clear that the mounds had actually been built by the Native Americans who had been summarily cleared out of the American midwest, the effigy and burials mounds were destroyed in huge numbers, and cities and farmsteads built in those same locations.
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