As with everything in beekeeping, there’s more than one day to mark a queen, but most methods usually involve catching the queen, holding her down in some way so she can’t move, and then dabbing her with a paint pen or marker.
I’ve never bothered marking queens myself because, until now, I’ve been pretty free wheelin’ with my queens. I usually have little need to hunt them down. But this year I had a colony that was ready to swarm and it would have been great if I could have found the queen then. A marked queen in a few other situations would have made my life easier too. So I got myself one of the new fan-dangled queen catchers and I marked a few queens, the first time I’ve done this in 10 years. Here’s a video that shows how I did it: