They are replicas but beautiful nevertheless. If u want to see the real ones check out the ones in the southwest part of the state.
From what I saw, they are replicas. They are well done, so it is very good for providing a visual concept of what they were like. I grew up in Northern Arizona, and went to Wapatki quite often, those are genuine, and you can see the difference between the two. The museum portion does have some artifacts of pottery and other day to day items which rounds out the experience.
The official history states that it was legitimate procedure of the relocation of the cliff dwellings (which is sounds really weird, even if they tried to cover it up with good moral ideas), the ruins of original dwellings were relocated and restored in the beginning of XX century, so I guess we can call it a "replica", specially after the original architecture of the dwellings was reassembled with an add-ons...
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