Two complementary DNA (cDNA) clones (pTK-1 and -2) encoding two distinct isotypes of mouse Mg(2+)-dependent protein phosphatase beta (MPP beta-1 and -2, respectively) were isolated from a melanocyte cDNA library. Although mouse pTK-1 is orthologous to the rat cDNA (JW5) reported previously [Wenk, J., Trompeter, H.I., Pettrich, K.G., Cohen, P.T.W., Campbell, D.G., and Mieskes, G. (1992) FEBS Lett. 297, 135-138], pTK-2 is a novel cDNA clone. It was strongly suggested that the pTK-1 and -2 cDNAs are splicing variants of a single pre-mRNA. The difference in the amino acid sequences between MPP beta-1 and -2 was observed only at the carboxy-terminal regions. Both the recombinant MPP beta-1 and -2 expressed in Escherichia coli cells were immunoreactive to an anti-MPP beta antibody and exhibited Mg(2+)-dependent and okadaic acid-insensitive protein phosphatase activities with similar substrate specificities. Although the mRNA of MPP beta-1 was expressed ubiquitously in various mouse tissues, that of MPP beta-2 was expressed exclusively in brain and heart. These results suggest the difference in the physiological roles of these two enzyme isotypes.