As a toxic nitrogenous waste, ammonia causes ionoregulatory and neuronal dysfunction in aquatic animals. Without mechanisms to convert ammonia into less toxic molecules such as urea and uric acid, ammonotelic animals excrete ammonia directly into the surrounding environment. In order to deal with conditions causing possible elevated hemolymph ammonia levels, such as feeding, an efficient ammonia excretion process must be in place to keep the hemolymph ammonia levels within a tolerable range. While the excretory mechanisms of ammonia have been investigated in detail in fish and crustaceans, the intracellular regulation of these processes is basically unknown. To investigate the involvement of two key pathways, the cAMP/PKA and cGMP/PKG pathway, in the ammonia excretion process, gills from osmoregulating green shore crabs, Carcinus maenas, were isolated and perfused with hemolymph-like solutions containing either 200 µmol L-1 or 500 µmol L-1 NH4Cl, mimicking the hemolymph ammonia levels in the resting state and after feeding, respectively. Basolateral application of the adenylyl cyclase activator or membrane-permeable 8-Bromo-cAMP, caused a significant decrease in the ammonia excretion rate. In addition, after PKA activation by 8-Bromo-cAMP, metabolically generated ammonia increased and the majority was now transported towards the hemolymph and not, as seen under control conditions, into the environment. Together, this suggests that the cAMP/PKA pathway promotes an ammonia retention mechanism. In contrast, activating the cGMP/PKG pathway by the application of membrane-permeable 8-Bromo-cGMP, resulted in an increase of the transbranchial ammonia excretion rate, which could be blocked by the PKG inhibitor KT5823. In addition, participation of nitric oxide synthase (NOS) in the cGMP synthesis via the soluble guanylyl cyclase is suggested due to the observed inhibitory effect on the branchial ammonia excretion after basolateral application of the NOS inhibitor L-NAME. In conclusion, cGMP/PKG pathway, not the cAMP/PKA pathway promotes transbranchial ammonia excretion across the gill epithelium in C. maenas. The cAMP/PKA pathway is involved in a so far undescribed ammonia retention mechanism. The provided data will offer a basis for new venues investigating epithelial ammonia transport processes in general.