Mn2+ concentration affecting polycyclic aromatic hydrocarbon pyrene degradation by the Flavobacterium sp. FCN2 was investigated by adding Mn2+ during several periods, which including bacteria cultivation period, bacteria degrading pyrene and enzymatic degradation period. Results show the concentration of Mn2+ was beneficial for pyrene degradation, and Mn2+ was no influential to bacteria growth and magnitude. When Mn2+ was added during culturing strain FCN2 period, bacteria FCN2 can enrich Mn2+, and pyrene removal efficiency by Mn2+ enrichment bacteria is 1.26 times more than that of without Mn2+ enrichment bacteria. As well as the situation that adding Mn2+ during FCN2 degrading pyrene period that pyrene removal efficiency is 1.67 times more than that of without Mn2+. And when adding Mn2+ during enzymatic degradation periods, the elimination efficiency of pyrene was 1.30 times more than that of without Mn2+.