Unique Serial Number for Atmel SAM Series
The SAMD21 processors do indeed have a unique ID, as explained in the "Serial Number" section in the "Memories" chapter in the Atmel SAMD21 datasheet. (This is currently section 10.3.3, page 46). The datasheet states


  Each device has a unique 128-bit serial number which is a
  concatenation of four 32-bit words contained at the following
  addresses:
  Word 0: 0x0080A00C
  Word 1: 0x0080A040
  Word 2: 0x0080A044
  Word 3: 0x0080A048
  The uniqueness of the serial number is guaranteed only when using all 128 bits.


USB devices are expected but not required to provide a serial number, but I am not aware of any microcontroller USB peripheral that incorporates a serial number directly—all the USB peripherals I know of merely allow the processor, if desired, to provide the serial number as part of the descriptor.