M. validus, once thought to be the type species of Machaeroprosopus, was named in 1916 on the basis of three complete skulls from Chinle Formation, Arizona.

Thus, Machaeroprosopus was considered to be a nomen dubium or "doubtful name" because of the lack of diagnostic specimens that can support its distinction from other phytosaur genera.

[11] Stocker and Butler (2013) also treated M. andersoni as a valid species,[11] and not a junior synonym of Machaeroprosopus buceros as was previously suggested by Long and Murry (1995).

[5] This taxon was considered to be a junior synonym of M. buceros by Long and Murry (1995) and later authors,[5][12][2] although Stocker and Butler (2013) treated M. andersoni as a valid species.

It was collected from the Norian-aged Petrified Forest Member of the Chinle Formation, at the Arroyo Seco drainage, Orphan Mesa in the Rio Arriba County of New Mexico.

[10][11] Following the revision, M. andersoni was treated as a valid species by Stocker and Butler (2013),[11] and not a junior synonym of Machaeroprosopus buceros as was previously suggested by Long and Murry (1995).

[11][3] M. jablonskiae was first described and named by William G. Parker and Randall B. Irmis in 2006, on the basis of the holotype PEFO 31207, posterior skull roof and braincase missing the rostrum and palate.

It was collected in September 2002 from the lower Jim Camp Wash beds, Sonsela Member of the Chinle Formation, at locality PFV 295, near Mountain Lion Mesa in Petrified Forest National Park, Arizona.

The skulls were collected at Patricia Site (TTU Vertebrate Paleontology Locality 3870), 13 km South of Post, Garza County of west Texas, from the upper unit of the Norian Cooper Canyon Formation, Dockum Group.

Other vertebrates known from this site include TTU-P10074, a partial skull referred to Machaeroprosopus sp., a phytosaur postcranial skeleton, fish, a temnospondyl amphibian, Typothorax, Postosuchus, Shuvosaurus and a theropod dinosaur.

[3] M. mccauleyi was first described and named by Karen A. Ballew in 1989 as a species of Pseudopalatus, on the basis of the holotype UCMP 126999, an incomplete skull, lacking the anterior half of the rostrum, and probably associated lower jaws.

[8] It was collected at Dry Creek Tank SE (also known as UCMP V82040, UCMP 7043 and PFV 55), Apache County of Arizona, from the Norian-aged Upper Petrified Forest Member / Formation according to most authors,[8][11][5] or possibly Sonsela Member of the Chinle Formation according to Parker & Irmis (2005).

Ballew (1989) also referred to this species USNM 15839, another incomplete skull lacking the anterior half of the rostrum from Arizona.

[5] Long and Murry (1995) also suggested that Redondasaurus gregorii from the Redonda Formation of New Mexico is a junior synonym of M. pristinus,[5] although this was not accepted by subsequent authors.

Thus, Machaeroprosopus was considered to be a nomen dubium or "doubtful name" because of the lack of diagnostic specimens that can support its distinction from other phytosaur genera.