The previously recognised original description of Crocodilus johnsoni Krefft, 1873 in the Proceedings of the Zoological Society of London is antedated by several months by a newspaper article penned by Krefft, in which the species is named as Crocodilus johnsonii. The same article validates the name Tomistoma krefftii, previously considered a nomen nudum. Tomistoma krefftii is a junior objective synonym of Crocodilus australis Krefft, 1867, both based on a dried head collected by William Woods near Burketown, Queensland. Both of these names potentially imperil stability of nomenclature of Crocodylus johnstoni, but the latter name is a nomen protectum, and the emendation of johnsonii to johnstoni is to be maintained due to prevailing and current usage. Crocodilus australis Krefft, 1867, a nomen oblitum with respect to C. johnstoni, is further a senior homonym in the genus Crocodylus of Oophilus porosus var. australis Gray, 1867 (another previously overlooked name), Crocodilus australis Bravard, in Burmeister, 1885, a Miocene fossil species from South America, currently in Caiman, and Crocodylus porosus australis Deraniyagala, 1953. The type specimen of Crocodilus australis Krefft is lost, but a contemporaneous archival photograph of what is presumed to be the specimen has been located. The holotype of Crocodilus johnsonii, originally described as just a skin, is redefined to include both the mounted skin (now missing the head) and an accompanying skeleton (now missing a skull), both bearing corresponding damage from a bullet wound at the time of collection. Archival photographs of the entire mounted skin, corresponding to a photograph sent to John Gray at the British Museum by Krefft in 1873 and to a cast of the head sent to Gray the following year, provide evidence that the head was removed from the mounted skin for casting shortly after the description of the species, and subsequently lost. A justification is provided, based on historical documentation, for the often emended type locality of C. johnstoni from the original Cardwell to Cashmere, Queensland.