When you’ve found the queen in your beehive, it’s a good idea to mark her so that you can easily find her in future. The best time to find and mark her is at the first inspection in spring when fewer bees are in the hive than in summer. A colour code enables you to tell the age of the queen; you can use white correction fluid because it shows up better than colours. Your hive record card should show the age of your queen. If you find an unmarked queen in the hive you know the original one has been replaced so you mark her and alter the date on the card.
Here are some methods of marking the queen.
Pick her from the comb by the wings using your right hand. (You can’t do this wearing gloves.) Transfer her to your left hand and hold her thorax between your finger and thumb. Never hold her by her abdomen. Mark her on the thorax and then release her back onto the comb. Practise on some drones to gain confidence in handling bees before attempting to mark a queen.
Use a queen marking cage which presses into the comb to confine the queen. Hold the cage over the queen and move her away from brood before pressing it into an area of stores or empty cells. With your marker ready in your right hand gently press the cage down just enough to hold the queen still, mark her thorax and lift the cage off straight away. Again, practising on some drones can help you acquire the knack of holding a bee still.
Alternatively, you can buy tube and plunger queen marking cages where you can gently push the queen into the tube and then up against the mesh at the top where you can mark her thorax through the mesh.
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Source:http://www.dummies.com/how-to/content/marking-your-queen-bee.html
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