In this study, the characteristics of organic phosphorus (Po) fractions in sediments of six lakes from the middle and lower reaches of Yangtze River region and Southwestern China Plateau, China were investigated using a soil Po fractionation scheme, and the relationships between Po, inorganic phosphorus (Pi) and pollution status were also discussed. The results show that the rank order of Po fractions was: residual Po>HCl-Po>fulvic acid-P>humic acid-P>NaHCO3-Po, with their average relative proportion 8.7:4.6:3.2:2.1:1.0. Po fractions, especially nonlabile Po, were significantly correlated with organic matter, Po and NaOH-Pi. Different distribution patterns of P fractions were observed in those two different regions. Po fractions in the heavily polluted sediments were higher than those in moderately and no polluted sediments, it is suggested that Po should be paid more attention in the lake eutrophication investigation.