Amphibious mudskippers (Oxudercidae) exhibit diverse feeding adaptations that facilitate exploitation of dynamic intertidal habitats, yet trophic-related digestive morphology remains poorly documented for several species. This study provides the first comprehensive assessment of digestive morphology associated with feeding in the mudskipper Scartelaos histophorus from coastal mudflats of the Mekong Delta, Vietnam. A total of 135 specimens were examined to characterize oral structures, dentition, gill apparatus, and gastrointestinal morphology. Scartelaos histophorus exhibited morphological traits indicative of an omnivorous feeding strategy with a tendency toward benthic animal prey. Allometric modeling of log-transformed intestinal length, with standard length as a covariate, revealed significant effects of body size, sampling site, and sex × site interaction, whereas sex alone was not significant. Principal component analysis of size-adjusted traits identified two major axes of feeding-related morphology, corresponding to pharyngeal tooth-plate/toothheight variation and jaw–intestinal morphology. These findings offer new insights into the ecological diversification of mudskippers and provide a morphological basis for understanding feeding ecology and trophic adaptation in amphibious gobies inhabiting intertidal mudflat ecosystems.

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