Clean the crack. Don't use water, as this will add to the moisture content of the wood. Instead, use a scraper to scrape out trash and the hose from a vacuum cleaner to get as much debris out of the crack as possible. The cleaner you can make the crack, the more likely it is that the repair will hold.
Apply a latex wood filler to the crack. Be wary of applying too much, though. When the wood filler dries, it will expand and make your crack larger -- just the opposite of what you want to achieve. Just apply a thin line of the filler in the crack to help seal the gap in the wood. Allow it to dry according to the directions on the product; each brand may have its own drying time.
Restain that area of the floor. If you want to ensure that the patch of floor repaired matches the rest of the coloring of the subfloor, you can restain it. However, this may not be as necessary as it would be for the top panels, since that is what you see when the floor is complete.