I think RFID technology can be combined with infrared. Try to search for RTLS chip. What I do not know if the chips are small and cheap enough as RFID...

I think infrared markers will be a better solution. You can search it online.

Moreover in thermal images too location of any particular object can be identified using tracking software. But I think the former is a better solution.

See the links below.

http://labs.biology.ucsd.edu/nieh/papers/SadlerNieh2011.pdf

http://www.sciencedirect.com/science/article/pii/S0040603112000512

Thanks a lot the RFID we used on bees just have a short range, but I have some left over and I will try it - Thanks Barid for the paper seems promising

Try silver paint to make dots like morse code or lines like I Chi characters. The low emissivity with be seen in IR as lower temperature, although the temperature will be the same. Application is the challenge.

Thanks a lot - the application might be not such a problem, since we mark them on the thorax any way with different colour codes

Any IR radiometer (Camera with temperature measuring capability) can be used. I imagine mounting the camera, say a FLIR A series unit, which can be operated remotely using a LAN connection and software to record video or capture individual images, E.g. FLIR researcher software. No need to use a Digital camera if the IR unit can identify the individual markings on the bee. But it can be done if the times in each camera is synced. Then just compare images from the same time, to a fraction of a second. What are you trying to achieve? Time for a bee to enter and exit the hive?