It could mean an unknown number of thousands of years e.g 'tens of thousands of years' or 'hundreds of thousands' as previously suggested. However, the word 'unknown' could also refer to the San themselves or their routine behaviour of showing respect to animals (or whatever else).
I agree with polyamede; we need more context. It seems more likely that it means that the number of years is unknown, but it could also mean that that the San were unknown thousands of years ago. (If it is the latter, then And is correct, not An.)
(And, along with context, we need the source of this quotation.)