Understanding aspects of development in animals posessing certain “ancestral” traits can provide key insights into the evolution of various larval forms of invertebrates. Little is presently known concerning the neurodevelopment of Protobranchia, a group of bivalve mollusks. We are first to demonstrate that neurogenesis of the pericalymma larvae of the protobranch Acila insignis differs dramatically from that of the larval nervous system of autobranchia species as revealed by serotonin (5-HT) and FMRFamide antibodies and whole-mount confocal microscopy. Early in the development of pericalymma, two and then three flask-shaped cells immunopositive for 5-HT appear in the apical organ (AO). Later on, in mid-stage larvae, cells immunostained for FMRFamide appear in the dorsal portion of the larva, including a weak signal in the AO. Immediately prior to metamorphosis, the larval FMRFamide-ergic nervous system consists of a single cell in the AO together with several non-sensory cells in the posterior and dorsal regions. No neuronal connections between the larval neuronal cell groups were observed. However, despite the obvious differences in early neurogenesis, there are clear neuromorphological similarities of the studied protobranch species to (1) spiralians (by the presence of an AO), (2) certain trochozoans (by peripheral cells containing FMRFamide) and (3) bivalve mollusks (by AO including three flask-shaped cells revealed by immunostaining for 5-HT). Thus, the nervous system of A. insignis is similar to that of other mollusks and lophotrochozoans due to the presence of an AO, while differing from all the studied groups in other characters (location and composition of FMRFamide cells). Morphological and molecular development of key protobranch taxa need to be further studied in order to infer the evolution of mollusks.