The amount and distribution of nitrogen cycling bacteria in sediments of Meiliang Bay and Gonghu Bay of Lake Taihu were studied by FISH analysis. The amount of archaea decreased along the sediment depth, however, its ratio to total microorganisms increased. The amount of Ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) in Meiliang Bay was higher than that in Gonghu Bay although the amount of both bacteria decreased along the sediment depth. Our results indicated that the existence of aquatic macrophyte in Gonghu Bay might affiliate transformation of nitrogen. Crenarchaeota was universally detected in surface sediments and overnumbered AOB, which indicated that it might play an important role in nitrogen cycling.