On the basis of the conserved amino acid sequences of the catalytic domain of both soluble and plasma membrane forms of guanylyl cyclase, we have used the polymerase chain reaction to identify a new form of guanylyl cyclase that is expressed principally in kidney. The cDNA for this new form (GC-S beta 2) codes for a 76.3-kDa protein, which most closely resembles a 70-kDa subunit (GC-S beta 1) of the lung soluble guanylyl cyclase. The mRNA for GC-S beta 1 is preferentially expressed in lung and brain, whereas GC-S beta 2 mRNA is more abundant in kidney and liver. An 86 amino acid carboxyl-terminal region extends beyond the C-terminus of GC-S beta 1 and contains a consensus sequence (-C-V-V-L) for isoprenylation/carboxymethylation. This is the first demonstration of heterogeneity among the heterodimeric forms of guanylyl cyclase and suggests differential regulation.