Conventional soluble guanylyl cyclases form alpha/beta heterodimers that are activated by nitric oxide (NO). Recently, atypical members of the soluble guanylyl cyclase family have been described that include the rat beta2 subunit and MsGC-beta3 from Manduca sexta. Predictions from the Drosophila melanogaster genome identify three atypical guanylyl cyclase subunits: Gyc-88E (formerly CG4154), Gyc-89Da (formerly CG14885) and Gyc-89Db (formerly CG14886). Preliminary data showed that transient expression of Gyc-88E in heterologous cells generated enzyme activity in the absence of additional subunits that was slightly stimulated by the NO donor sodium nitroprusside (SNP) but not the NO donor DEA-NONOate or the NO-independent activator YC-1. Gyc-89Db was inactive when expressed alone but when co-expressed with Gyc-88E enhanced the basal and SNP-stimulated activity of Gyc-88E, suggesting that they may form heterodimers in vivo. Here, we describe the localization of Gyc-88E and Gyc-89Db and show that they are expressed in the embryonic and larval central nervous systems and are colocalized in several peripheral neurons that innervate trachea, basiconical sensilla and the sensory cones in the posterior segments of the embryo. We also show that there are two splice variants of Gyc-88E that differ by seven amino acids, although no differences in biochemical properties could be determined. We have also extended our analysis of the NO activation of Gyc-88E and Gyc-89Db, showing that several structurally unrelated NO donors activate Gyc-88E when expressed alone or when co-expressed with Gyc-89Db.