The tetrapodomorph fish Marsdenichthys longioccipitus from the Givetian-Frasnian of Mt. Howitt, Victoria, Australia, occupies an uncertain phylogenetic position. Marsdenichthys has been linked to the base of the Tristichopteridae, as well as to the poorly known Northern Hemisphere form Rhizodopsis, based on the presence of rounded scales bearing a median boss on the internal surface. However, its affinities to these taxa are ambiguous, due to the incomplete preservation of the two Marsdenichthys specimens initially described. For the first time, we present significant information regarding the cheek and palate of Marsdenichthys, based on the descriptions of two new specimens from Mt. Howitt. New autapomorphies for Marsdenichthys are proposed, including the presence of a bar-like maxilla being approximately equal in depth to the dentary, and a rectangular anterior termination of the lacrimal. Several plesiomorphic features are described from the palate, including rounded vomer morphology lacking a posterior process, a relatively short, broad parasphenoid, and a dermopalatine approximately equal in length to the ectopterygoid. No synapomorphies are shared between Marsdenichthys and tristichopterids. Scale morphology is redescribed, and shown to exhibit concentric rings on the external surface, as in Rhizodopsis. However, differences in skull morphology, such as the lack of an external opening for the pineal foramen in Rhizodopsis, suggest that this scale morphology may have evolved independently.