We hypothesise that the body shapes of three mudskipper species (Boleophthalmus dussumieri, Periophthalmus waltoni, and Scartelaos tenuis) are ecomorphological adaptations to different epi- and infaunal habitats. We investigated: (i) the association between burrow density and selected ecological variables; (ii) the phylogenetic relationships among these species, based on two mtDNA and one nDNA markers; (iii) their geometric morphometrics and ancestral shape reconstructions, based on two-dimensional landmark configurations; and (iv) their body surface-to-volume ratios (SAV), based on a geometric model. Boleophthalmus dussumieri and S. tenuis are more closely related, and more elongated than P. waltoni; the body of S. tenuis also has a higher SAV, and its elongated shape appears to be a divergent trait. P. waltoni is found in a wide range of conditions, including vegetated habitats; B. dussumieri is associated with low-energy conditions and fine unvegetated deposits; and S. tenuis is associated with high-energy conditions and coarser, non-cohesive sediments. These results suggest that body elongation in Scartelaos species is a divergent locomotory adaptation to marine habitats characterised by semi-liquid and less cohesive sediments. The more compact body shape of Periophthalmus species is hypothesised to have evolved from a gobionelline ancestor, and is proposed to be a preadaptation to subaerial locomotion in semi-terrestrial habitats.