The Ophidiidae is a group of more than 300 species of fishes characterized by elongated, snake-like bodies and continuous dorsal, anal, and caudal fins. While describing a new species in the genus Monomitopus, we discovered a bilaterally paired fenestra on the dorsomedial surface of the neurocranium. We surveyed the distribution of this fenestra across species of Monomitopus and previously hypothesized allies in the genera Dannevigia, Dicrolene, Homostolus, Neobythites, and Selachophidium, finding variation in its presence and size. We also found a prominent bilaterally paired lateral fenestra and a posterior expansion of the exoccipital in the neurocrania of M. americanus and S. guentheri, with soft tissue connecting the back of the neurocranium to the first epineural and pectoral girdle in S. guentheri. In this study, we describe the distribution of and variation in these features. We integrate morphological characters and DNA data to generate a phylogeny of Monomitopus and allies to understand their relationships and trace the evolutionary history of these novel features. Our results call the monophyly of Monomitopus into question. The presence of the lateral neurocranial fenestra and posterior expansion of the exoccipital support the reclassification of M. americanus as a species of Selachophidium.