We found many isoforms of membrane-bound guanylyl cyclase (membrane GC) in the gonads of several echinoid species including Hemicentrotus pulcherrimus (six isoforms), Glyptocidaris crenularis (four isoforms), Clypeaster japonicus (three isoforms), Diadema setosum (three isoforms), and Brissus agassizii (three isoforms). In addition to these membrane GC isoforms, several putative soluble GC isoforms were also found, one in H. pulcherrimus, two in G. crenularis, and three in D. setosum. Other echinoderm species also possess many GC isoforms in their gonads: the starfish, Asterina pectinifera, has five membrane GC isoforms; the brittle star, Ophioplocus japonicus, possesses six membrane and two putative soluble GC isoforms; and the sea cucumber, Stichopus japonicus, contains five membrane and two putative soluble GC isoforms. We also obtained the full-length cDNA sequence of some of these isoforms, one for sperm-activating peptide (SAP) receptor-type GC, and the other for a homolog of the vertebrate natriuretic peptide receptors/membrane GCs, and analyzed their phylogenetic relationship among various invertebrate and vertebrate GC isoforms.