Oxudercine gobies include fully aquatic to highly terrestrial species. In this study, we investigated the anatomy of the feeding apparatus of two species, Parapocryptes serperaster and Pseudapocryptes elongatus, both of which can be regarded as representing early stages of the transition from an aquatic to a terrestrial existence. The feeding system of these two species is morphologically similar: they both exhibit a unique orientation of premaxillary (vertical) and dentary (horizontal) teeth; a heterogeneous development of gill rakers among gill arches; strongly curved, large pharyngeal plates studded with numerous papilliform teeth; branchial basket skeletons with nearly equal gill-arch lengths; and a similar configuration of the branchial basket musculature. On the other hand, the number of teeth in Pa. serperaster is more than twice that in Pd. elongatus, both on the premaxillary and dentary bones, while the size of the teeth in Pa. serperaster is only half that in Pd. elongatus both in length and width. Pharyngeal plates and associated muscular and skeletal elements are more posteriorly positioned in Pd. elongatus. These similarities and differences may be explained by different trophic adaptations to herbivory and omnivory during the early transitional stages to life on mudflats. The results are discussed in the context of the two phylogenetic hypotheses of the oxudercine gobies based on their ecology and morphology and on genetic analysis.