I have some that are marked, and some that are not. I like them to all be amrked, so I can easily see them when I'm moving frames around, but i don't go very far out of my way to mark them. If i see them and tehy are calm, then maybe they get marked. if i don't see them, then i don't go searching for them simply to mark them. Thr only real benefit i can see to having a marked queen is to keep track of genetics and know when a supercedure has taken place.
I started marking queens when I started raising my own. I use the normal colors for each year. I can tell if a hive decides to replace a queen. Before, sometimes I knew a hive was having an issue, but since I'm not in my hives every day or week it was hard to tell exactly what was going on. So sometimes I would buy a queen to replace the one in the hive not realizing that I just replaced a supersedure queen that was just mated. Now it's easy to tell if I have a new queen. Also it makes finding the queens, especially the darker ones, easier.
I mark mine with colored paint, from water-based paint marker pens, usually uni POSCA paint pens. Marking queens is part of my queen rearing process. I mark queens as I verify that a virgin has begun to lay. That way I know that if I see a marked queen, that she had begun laying, and is most likely mated.
Mann Lake has a Queen Marking Tube for $6.25. Makes marking queens a lot easier. Make sure that the paint is dry on your queen and that you puff smoke around her as you reintroduce her to the hive or they will ball her and kill her since her pheromone has changed.
I've never seen nor heard of them killing the queen if you don't use smoke before. I merely wait for the paint to dry and release her with no troubles. As for troubles, make sure you test your pen right before you use it. If it heats up in the sun and you think you're dabbing a little on the back of the queen, the pen could have become pressurized due to the warmth of the sun and paint will go everywhere. That I have seen and the queen was superceded within a week. That was a hard learned lesson and now my bee supply box that I carry while working the hive has colored spots (and drips and splotches from then they've gotten hot) all over the top from where I always test the pens.
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