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According to the schematics, the Arduino Due has two USB inputs:

  1. Native
  2. Programming

Why is this? And when would I use the different ports?

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Is there a mapping of the native port to serial pins? The programming port maps to 0 and 1 correct? – user3233 Jul 20 '14 at 1:15
up vote 6 down vote accepted

Either port can be used for programming, but the native USB port lets you do other things:

It also enables the Due to emulate a USB mouse or keyboard to an attached computer. To use these features, see the Mouse and Keyboard library reference pages.

The Native USB port can also act as a USB host for connected peripherals such as mice, keyboards, and smartphones. To use these features, see the USBHost reference pages. http://arduino.cc/en/Main/arduinoBoardDue

So you can use the Due to interface with USB devices or connect it to your computer and have it act like a USB device.

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So, it would be possible to attach a mouse to USB native, and detect and Register mouse movements in the host laptop via the other USB input? – poseid May 19 '14 at 11:40
    
I think only the native one can do both of those things. The other one is for programming only. – sachleen May 19 '14 at 18:13

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