stimmer:
The native USB port does not trigger a reset on opening the serial monitor - if it did it would cause a USB disconnect. If you need auto-reset on opening the serial monitor, use the programming port.
Makes sense. But what is this all about? It can be found in arduino documentation.
"Opening and closing the Native port at a baudrate other than 1200bps will not reset the SAM3X. To use the serial monitor, and see what your sketch does from the beginning, you'll need to add few lines of code inside the setup(). This will ensure the SAM3X will wait for the SerialUSB port to open before executing the sketch:
while (!Serial) ;"