Fluorescent proteins especially green fluorescent protein (GFP) and red fluorescent protein (RFP) are ones of the widest markers in application these years. They can produce fluorescence and were obtained from water biology, GFP was obtained from Aequorea victoria and RFP from Discoma coral. Their structure and luminescence principle are similar, and with the same molecular weight 28kDa. Chromosome marker and plasmid marker are two kinds of way to mark biology. They have been applied widely in protein-protein interactions, screen positive clone, orientation, function and biology of protein factor, ecology of microorganism and so on.