Microcystins (MCs) are well known worldwide as hepatotoxins produced by cyanobacteria, but little is known about the physicochemical properties of these compounds. The dependence of the n-octanol/water distribution ratio (DOW) of MC-RR and -LR to pH was measured by high-performance liquid chromatography combined with mass spectrometry (LC-MS). There was a remarkable difference in such relationships between MC-RR and -LR. The log DOW of MC-LR decreased from 1.63 at pH 1.0 to -1.26 at pH 6.5, and stabilized between -1.04 and -1.56 at a pH of 6.5 similar to 12.0; log DOW of MC-RR varied between -1.24 and -0.67 at a pH of 1.00 similar to 4.00, and stabilized between -1.20 and -1.54 at a pH of 4.00 similar to 12.00. The difference of hydrophobicity in acidic condition between MC-RR and -LR is important, not only for the analytical method of both toxins, but perhaps also for understanding the difference of toxicity to animals between the two toxins.