Although the lophophore is regarded as the main synapomorphy of all lophophorates, the evolution of the lophophore in certain groups of lophophorates remains unclear. To date, the innervation of the lophophore has been studied with modern methods only for three brachiopod species belonging to two subphyla: Linguliformea and Rhynchonelliformea. In the third subphylum, the Craniiformea, there are data for juveniles but not for adults. In the current research, the innervation of the lophophore in Novocrania anomala adults was studied by immunocytochemistry and confocal laser scanning microscopy. In the spiral lophophore of adults of the craniiform N. anomala, each arm is innervated by six brachial nerves: main, additional main, accessory, second accessory, additional lower, and lower brachial nerves. Compared with other brachiopod species, this complex innervation of the lophophore correlates with the presence of many lophophoral muscles. The general anatomy of the lophophore nervous system and the peculiarities of the organization of the subenteric ganglion of the craniiform N. anomala have a lot in common with those of rhynchonelliforms but not with those of linguliforms. These findings are consistent with the “Calciata” hypothesis of the brachiopod phylogeny and are inconsistent with the inference that the Craniiformea and Linguliformea are closely related.