The recent discovery and description of an unusually puzzling catfish, Kryptoglanis shajii Vincent and Thomas (2011) from ground and surface waters in Kerala State, southwestern, peninsular India, added an unresolved taxon to the order Siluriformes. Here we use high-resolution X-ray computed tomography (HRXCT) and X-radiography to illustrate, describe and compare the bony skeleton of Kryptoglanis with the objective of determining its phylogenetic position.Several characteristics of Kryptoglanis are strongly modified and structurally complex, setting this catfish apart from other siluriforms. Striking examples are its greatly shortened mesethmoid with overlapping frontals; non-tubular nasal bone; absence of the infraorbital lateralis sensory canal and canal bones but with an apparent antorbital bone; the flat and expansive orbitosphenoid; the vaulted supraoccipital-Weberian neural arch joint; the fenestrated occipital wall; the upwardly flexed occipito-vertebral joint; three pairs of elongated accessory processes off the compound Weberian vertebra; a unique exoccipital process for attachment of the transscapular ligament; hyomandibular-sphenotic ball and socket articulation; a serially notched anterior ceratohyal; and a novel posttemporo-supracleithum joint with the fourth transverse process. Some of these apparent autapomorphic features may eventually be found in some other siluriforms and judged to be informative on phylogenetic relationships. Presently, however, we have identified a few features that support the placement of Kryptoglanis in the Siluroidei (the presence of a posterior nostril barbel and position of the pterosphenoid along the anterior margin of the trigeminofacial foramen), and therein, as the sister lineage to family Siluridae (the nodular form and small size of the autopalatine).