I have two Arduino Pro Mini 5V and two 3.3V. Now I soldered one 3.3V to a board and a 5V, but I forgot which one is which and I can't see below to see which of the boxes is checked. I have two reference ProMinis, but couldn't detect a difference so far.
Since there is an on-board regulator, apply a voltage to the RAW pin and measure VCC.
Ideally you should apply >6V. Even if you only have 5V source available you can probably still tell the difference between the 3.3 and 5 boards. (The 3.3V board will be 3.3V with 5V on RAW while a 5V board will be something less, probably around 4).