The classification of tomistomines among Crocodylia has been in flux; while traditionally thought to be within Crocodyloidea, molecular evidence indicates that they are more closely related to true gharials as members of Gavialoidea.

The splenial bone of the lower jaw is long and slender, forming a distinctive "V" shape not seen in gharials.

Several early tomistomines are found in coastal marine deposits, suggesting that they lived along the shoreline or in estuaries.

During this time, the Indian subcontinent was separated from mainland Asia, creating a barrier to species that could not tolerate salt water.

A close relationship has been proposed between C. kuleri and D. zajsanicus from Belgium, suggesting that tomistomines migrated from Europe to the Americas through the De Geer land bridge connecting Norway to Greenland and the North American mainland or the Thule land bridge connecting Scotland, Iceland, Greenland, and the North American mainland.

Based on morphological studies of extinct taxa, the tomistomines (including the living false gharial) were long thought to be classified as crocodiles and not closely related to gavialoids.

[6] However, recent molecular studies using DNA sequencing have consistently indicated that the false gharial (Tomistoma) (and by inference other related extinct forms in Tomistominae) actually belong to Gavialoidea (and Gavialidae).

[7][4][8][9][10][11][12] Below is a cladogram from a 2018 tip dating study by Lee & Yates simultaneously using morphological, molecular (DNA sequencing), and stratigraphic (fossil age) data that shows the tomistomines belonging to Gavialidae, and that the members traditionally belonging to Tomistominae may in fact be paraphyletic with respect to the gharial:[11] Crocodyloidea/Crocodylidae Gavialis gangeticus Gharial Gavialis bengawanicus† Gavialis browni† Gryposuchus colombianus† Ikanogavialis† Gryposuchus pachakamue† Piscogavialis† Harpacochampsa† Toyotamaphimeia† Penghusuchus† Gavialosuchus† Tomistoma lusitanicum† Tomistoma schlegelii False gharial Tomistoma cairense† Dollosuchoides† Maroccosuchus† Paratomistoma† Kentisuchus†