Accurate quantification of aerobic anoxygenic phototrophic bacteria (AAPB) is of crucial importance for estimation of the role of AAPB in the carbon cycling in marine ecosystems. The normally used method "epifiuorescence microscope-infrared photography (EFM-IRP)"is, however, subject to positive errors introduced by mistaking cyanobacteria as AAPB due to the visibility of cyanobacteria under infrared photographic conditions for AAPB. This error could be up to 30% in the coast of the East China Sea. Such bias should be avoided by either subtracting cyanobacteira from the total infrared counts or using a fiowcytometer equipped with specific detectors for discrimination between cyanobacteria and AAPB.