Motherboards with same serial numbers!!!

I highly doubt that's possible since that's what's used during the RMA process.  The Serial number is usually located on the side of one of the motherboard slots.
To answer your question - Yes, it's unique and no they can not be the same

What exactly are you trying to do?

It is possible that they are looking at a part number instead of a serial number - those could be the same.

2 different answers, still confused.
What I am trying to do is a security for my software, I want to make a unique identifier for users to generate keys based on it.

use the network card mac address. these are unique. serial numbers are not gaurenteed to be unique. On ibm/lenovo the are soft so they may be preserved when one is replaced. sometimes they get left as 0. in any case the numbers are only unique per model so two pcs of different models will often have the same number.

If you are coding on windows you can use guidgen to create a unique serial...

http://msdn.microsoft.com/en-us/library/kw069h38.aspx

Cannot using MAC, as MAC is changeable!!!