The easiest way to determine wood rot, is to test the surface with a sharp item. The tip of a knife blade, or the end of a small common screwdriver, pushed into the wood's surface, will detect the density and strength of the wood.

By testing different areas, you will find different results. If the tool tips easily penetrate the wood, then it's rotted and should be changed out. If the wood easily flakes apart and you can quickly dig a small hole, it is beyond its service life. When the surface is hard and not easily penetrated, then it is good for a continued service.

The most critical areas of rot usually occurs wherever the wood is against a frame member, or where attaching hardware affixes the wood in place. The hardware allows fluids to penetrate into the thickness of the wood, having framing directly against the wood, traps fluids and doesn't allow the wood to easily dry out. If the flooring wasn't protected by mats, the horses' shoes will easily erode the wood's surface, opening the grain and quickening the rotting process.

Just poke around a bit and you'll easily discover what's good and not.

First thing is when in doubt, replace it! You will never forgive yourself if your horse falls through a suspect piece of wood.

Now, what to look for. Large or multiple knot holes in a board can weaken the board especially if located between cross members. Splintering of the wood shows stress and weakening of the woods structure. A soft or spongy feeling board or section of a board is definitely a sign of board fatigue and the need to be replaced.

If you do decide to replace your floor, here is a helpful article http://backyardranch.com/Horse_Trailer_Repair_Part_1.htm

Hope that helps some, good luck!