Flow cytometry is a method of identification biological agents that has various applications. It has been applied for identifying many types of antigens in various materials, including environmental samples. Recently it has been noticed that this method could be used for molecular detection of biological agents. The purpose of this work was to apply flow cytometry with nested-PCR for the molecular identification of B. anthracis. Paramagnetic streptavidin-coated beads were used to capture the resulting fluorophore-labeled sequences. The results show that flow cytometry can be successfully used to detect specific fluorescein- dUTP and a biotin marked sequences.