Tomistoma schlegelii was traditionally classified within Crocodylidae. Its skull characters group it with crocodiles, and the slender snout was interpreted as an independent adaptation to catching fish, arising separately from the gharial's.
DNA sequence data from the 1990s onward consistently placed Tomistoma as the sister taxon of Gavialis, the gharial, rather than among crocodiles. Later analyses that combined molecular data with morphology, including calibration against fossils, reconciled the conflict in favour of the molecular result, and Tomistoma is now generally placed in Gavialidae. The morphological signal that misled earlier workers is thought to reflect convergent skull features shared by large-bodied crocodylians.
The species is Endangered, with a fragmented population in peat swamp forest that is being drained, burned and converted to plantation. Population estimates remain poor because the habitat is difficult to survey, and estimates of remaining mature individuals should be treated as rough. Where exactly the boundary of Gavialidae falls is still discussed.