I'm planning on putting some pure strain bluegills in my pond to hopefully improve the genetics. Is there a good way to mark or tag these fish so I don't remove them while fishing other bluegill out?

P65,

FWIW I do not have the knowledge to comment on whether what you are doing will improve the genetics of your pond, but if I wanted to identify a population of fish after stocking, IMO I would use one of the fin clip methods.

There also some tagging systems that you could use. Some of the tagging systems use colored tags so you can visually identify an entire "class" such as what you're trying to do. I've got a tagging system that has numbered tags from lakework.com because I wanted to see growth (and other info) fish. I am only using it on LMB and not sure of the size BG you plan to stock but these tags would be too big for BG <4-5 inches, I think.