Beekeepers have designated colors to identify queens born in specific years. This helps you pick out the queen quickly, and to figure out if your hive will need a new queen soon. Be sure to choose the right paint color before marking your queen.  Any acrylic-based paint is fine. Many beekeepers use model paint or even paint pens. White paint is used for queens marked in years ending in 1 or 6. If the year ends in 2 or 7, use yellow. Use red for years ending in 3 or 8. Green paint is used for years ending in 4 or 9. Use blue for years ending in 5 or 0. Bees can get agitated or even injured if you hold them too long, so be sure your paint is ready for marking before you pick up the queen. Keep the paintbrush or paint pen dipped and ready to go in your other hand or on a small table next to the hive. Gently pick up the queen by her wings or thorax. Be very, very careful when you pick her up--if she struggles, you can accidentally tear her wings or crush her. Some apiaries sell marking kits that let you confine the queen to a small plastic box during marking, but this isn’t a requirement. If you accidentally drop the queen, you’ll want her to fall back into the hive instead of in the grass or on your beekeeping suit. Keep the queen held over the hive the entire time you’re working with her. Dab a small dot of paint on her thorax, immediately between her two front legs. Put on enough paint to make your mark visible, but don’t use too much--you could gum up her wings or legs with dried paint. Some beekeepers prefer to clip the queen’s wings instead of marking her with paint, but this is optional. If you choose to do this, pick her up gently and trim the bottom quarter of both wings with a small set of beekeeping clippers.

Summary:
Choose the correct paint color. Prepare your paint supplies. Pick her up gently by the wings or thorax. Hold her over the hive. Put a small dot of paint on her thorax. Clip the tips of her wings (optional).