The liver-specific toxin microcystin-LR (MC-LR) is a potent inhibitor of type 1 (PP1) and type 2A (PP2A) protein phosphatases. A tritiated form of the toxin, [3H]dihydromicrocystin-LR ([3H]DMC-LR), was used to identify target proteins in cellular fractions prepared from rat liver homogenates. About 80% of the [3H]DMC-LR bound to proteins was in the cytosolic fraction, which contained essentially all of the PP2A. In contrast, much of the PP1 was found in particulate fractions, each with only a few percent of the total protein-bound [3]HDMC-LR. Protein-bound [3H]DMC-LR in the cytosol co-eluted with PP2A, but not with PP-1 from a DEAE-Sepharose column. Native forms of liver cytoplasmic PP2A and PP1 separated by aminohexyl-Sepharose adsorption showed similar sensitivity to inhibition by MC-LR, and bound [3H]DMC-LR proportional to the amount of phosphatase activity. The results indicate that [3H]DMC-LR can bind both PP2A and PP1 in the liver which must be important for microcystin-induced toxicity, but is recovered mainly bound to PP2A in the cytosol.