Martill and his team originally classified Irritator as a maniraptoran dinosaur in the clade Bullatosauria (a group no longer considered monophyletic), as a close relative to the feathered ornithomimosaurs and troodontids.
Given that its dental morphology, particularly long snout, and assumed fin-shaped crest were features unknown in "other" maniraptorans, the researchers erected the new family Irritatoridae within the clade.
They recognized Irritator's affinities with Spinosaurus, in that they both had similarly shaped and unserrated teeth, but noted that the latter's mandible would not conform with the front of Irritator's upper jaw, and that other non-avian dinosaurs like Compsognathus and Ornitholestes also bore no serrations on some or all of their teeth.
Some of these claims were questioned in 1996 by Kellner who found that Irritator's skull lacked the one autapomorphy (distinguishing feature) diagnosed in maniraptorans at the time, which was having its jugal (cheek) bone forming part of the antorbital fenestra.
He also pointed out that since Irritator challengeri's holotype lacked the tip of its snout, it would not be possible to know if Spinosaurus's dentary could complement it or not.
Based on comparisons with Spinosaurus, Kellner resolved Irritator as a spinosaurid and synonymized Irritatoridae with that family.
Irritator was then assigned to the Baryonychidae along with Angaturama, Baryonyx, Suchomimus, and Spinosaurus by Oliver W.M. Rauhut in 2003.
Thomas Holtz and colleagues in 2004 considered the Baryonychidae synonymous with Spinosauridae, and moved these genera to the latter family.
Most later revisions have upheld these classifications.
As spinosaurids, Irritator and Angaturama are placed within the superfamily Megalosauroidea, with Spinosauridae being a possible sister taxon to the Megalosauridae.

In 1998, Sereno and colleagues defined two subfamilies within the Spinosauridae based on craniodental (skull and tooth) characteristics.
They were Spinosaurinae, where they placed Spinosaurus and Irritator; and Baryonychinae, to which they assigned Baryonyx, Suchomimus, and Cristatusaurus.
Spinosaurines were distinguished by their unserrated, straighter, and more widely spaced teeth, as well as smaller first teeth of the premaxilla.
In 2005, Dal Sasso and colleagues assumed Irritator's nostrils as being located above the middle of the maxillary tooth row; more posteriorly than in baryonychines, but less so than in Spinosaurus.
Sales and Schultz in 2017 found that Irritator's nostrils were in fact positioned closer to the front of the jaw, as in Baryonyx and Suchomimus; this more forward nostril placement was typically considered characteristic of baryonychines.
Nevertheless, Irritator also bore unserrated teeth, a trait associated with spinosaurines.
Sales and Schultz thus noted that the Araripe Basin spinosaurids Irritator and Angaturama might represent intermediate forms between the earlier baryonychines and later spinosaurines, and that further research may eventually render the former a paraphyletic (unnatural) group.

Irritator is further distinguished from Baryonyx, Suchomimus, and Cristatusaurus by having slightly over half as many teeth in the maxilla, and from Spinosaurus due to its comparatively larger and more forwardly positioned nostril openings, which, unlike in Spinosaurus, are also formed by the premaxilla.
The narrow sagittal crest, which ends in a knob-like process above the frontals, is another autapomorphy separating Irritator from other spinosaurids.
Although Angaturama limai's snout is generally narrower than in other spinosaurids, this might be due to damage sustained by the fossil; the holotype appears partly crushed and broken on its lower margin, with some of the preserved teeth having been sectioned off along their length.
Therefore, Angaturama's only valid autapomorphy is its sagittal crest, which extends farther forwards on the rostrum and is more exaggerated than in other known spinosaurid skulls.



 
Topology A: Benson and colleagues (2009)
 
Topology B: Sales and Schultz (2017)
Martill and his team originally classified Irritator as a maniraptoran dinosaur in the clade Bullatosauria (a group no longer considered monophyletic), as a close relative to the feathered ornithomimosaurs and troodontids. Given that its dental morphology, particularly long snout, and assumed fin-shaped crest were features unknown in "other" maniraptorans, the researchers erected the new family Irritatoridae within the clade. They recognized Irritator's affinities with Spinosaurus, in that they both had similarly shaped and unserrated teeth, but noted that the latter's mandible would not conform with the front of Irritator's upper jaw, and that other non-avian dinosaurs like Compsognathus and Ornitholestes also bore no serrations on some or all of their teeth. Some of these claims were questioned in 1996 by Kellner who found that Irritator's skull lacked the one autapomorphy (distinguishing feature) diagnosed in maniraptorans at the time, which was having its jugal (cheek) bone forming part of the antorbital fenestra. He also pointed out that since Irritator challengeri's holotype lacked the tip of its snout, it would not be possible to know if Spinosaurus's dentary could complement it or not. Based on comparisons with Spinosaurus, Kellner resolved Irritator as a spinosaurid and synonymized Irritatoridae with that family. Irritator was then assigned to the Baryonychidae along with Angaturama, Baryonyx, Suchomimus, and Spinosaurus by Oliver W.M. Rauhut in 2003. Thomas Holtz and colleagues in 2004 considered the Baryonychidae synonymous with Spinosauridae, and moved these genera to the latter family. Most later revisions have upheld these classifications. As spinosaurids, Irritator and Angaturama are placed within the superfamily Megalosauroidea, with Spinosauridae being a possible sister taxon to the Megalosauridae.
In 1998, Sereno and colleagues defined two subfamilies within the Spinosauridae based on craniodental (skull and tooth) characteristics. They were Spinosaurinae, where they placed Spinosaurus and Irritator; and Baryonychinae, to which they assigned Baryonyx, Suchomimus, and Cristatusaurus. Spinosaurines were distinguished by their unserrated, straighter, and more widely spaced teeth, as well as smaller first teeth of the premaxilla. In 2005, Dal Sasso and colleagues assumed Irritator's nostrils as being located above the middle of the maxillary tooth row; more posteriorly than in baryonychines, but less so than in Spinosaurus. Sales and Schultz in 2017 found that Irritator's nostrils were in fact positioned closer to the front of the jaw, as in Baryonyx and Suchomimus; this more forward nostril placement was typically considered characteristic of baryonychines. Nevertheless, Irritator also bore unserrated teeth, a trait associated with spinosaurines. Sales and Schultz thus noted that the Araripe Basin spinosaurids Irritator and Angaturama might represent intermediate forms between the earlier baryonychines and later spinosaurines, and that further research may eventually render the former a paraphyletic (unnatural) group.
Irritator is further distinguished from Baryonyx, Suchomimus, and Cristatusaurus by having slightly over half as many teeth in the maxilla, and from Spinosaurus due to its comparatively larger and more forwardly positioned nostril openings, which, unlike in Spinosaurus, are also formed by the premaxilla. The narrow sagittal crest, which ends in a knob-like process above the frontals, is another autapomorphy separating Irritator from other spinosaurids. Although Angaturama limai's snout is generally narrower than in other spinosaurids, this might be due to damage sustained by the fossil; the holotype appears partly crushed and broken on its lower margin, with some of the preserved teeth having been sectioned off along their length. Therefore, Angaturama's only valid autapomorphy is its sagittal crest, which extends farther forwards on the rostrum and is more exaggerated than in other known spinosaurid skulls.


 
Topology A: Benson and colleagues (2009)
 
Topology B: Sales and Schultz (2017)
Irritator