In aquatic systems, phosphorus exists in various chemical forms, and they are dynamically transformed by biological processes or chemical reactions. Orthophosphate (Pi) is a major component of biopolymers, and microorganisms preferentially consume Pi and Pi containing compounds compared with other phosphorus compounds. Methylphosphonate (MPn) is an organic phosphorus compound that has lower oxidation state (+3: phosphorous) than orthophosphate (+5) and it is stable with C-P tough chemical bond. In freshwater lakes with low Pi concentrations, microorganisms might utilize organic phosphorus compounds such as MPn instead of Pi. We investigated the vertical profiles of Pi and MPn concentrations in Lake Biwa (mesotrophic) and Lake Saiko (oligotrophic) to discuss phosphorus cycling. Water samples were vertically collected in August (pelagic zone of Lake Biwa in 2021 and Lake Saiko in 2023). After filtration (0.2 μm membrane filters), Pi concentrations were quantified by ion chromatography, while MPn were concentrated by Fe (OH)3 co-precipitation and ion chromatography was used after elution of MPn from Fe (OH)3 with ammonium solution. Our results indicated that MPn and Pi concentrations were extremely low (< 3.1 nmol L-1) in the epilimnion of both lakes. Pi concentrations increased with depth in the hypolimnion. And MPn relatively remained constant below the thermocline in Lake Biwa. In Lake Saiko, Pi concentrations have increased around the benthic zone (886.6 nmol L-1). Based on these results, we suggested the dynamics of phosphorus in these lakes as follows: 1) the low phosphorus concentrations suggest that these lakes are strongly oligotrophic states in August, indicating that primary production is limited by phosphorus availability. In this case, Alkaline phosphatase may facilitate the breakdown of phosphate esters to supply Pi. In both lakes, Pi concentrations gradually increased with depth in the hypolimnion, suggesting that high molecular weight particulate phosphorus compounds originating from thermocline may undergo microbial degradation. 2) In the epilimnion, DO data suggests that planktonic autotrophic microorganisms are intensely photosynthesizing. As a result, Pi is preferentially consumed by them and MPn is secondarily consumed depending on Pi availability. 3) In Lake Biwa, MPn concentrations remained constant between 15-80 m, possibly indicating increased production of high molecular weight organic phosphorus compounds in the epilimnion compared to Lake Saiko. This study revealed that MPn and Pi concentrations were extremely low through the water columns in these lakes and suggested that Pi influences the distribution of MPn in Lake Biwa and Lake Saiko.