A sequence number would be standard. Have each side include an integer which increments each time a packet is sent. The receiver should discard any packet that contains a sequence number lower than the greatest one it has already processed.
Be careful about how wide you make the integer: if left long enough eventually it will overflow.
A timestamp can be treated as an integer sequence number: it does not matter what the integers "mean" as long as they are ever-increasing. The difficulty with saying that it will be a timestamp is that you start running into the problem that timestamps read out from the system are not necessarily unique if your processing is fast enough -- not unless you use a time routine that guarantees uniqueness (and some of them do.) But the time routines that guarantee uniqueness sometimes have to wait until the next "tick", which can slow down your processing.
The x64 architecture has a chip-level cycle count that is very tempting to use, as it would certainly be unique (until resets.) However it turns out that it takes several cycles to fetch that number from the processor; incrementing an integer is faster.
