The type species, Bothriospondylus suffossus, was described by Richard Owen in 1875. The specific epithetsuffossus means "undermined" in Latin, a reference to the fact that pleurocoels had hollowed out the sides of the vertebra. It is often incorrectly spelled as "suffosus". Owen based the species on holotypeNHMUK R.44592-5, a set of four dorsal vertebrae found in Wiltshire in stratum from the Kimmeridgian, the Kimmeridge Clay. Also three unfused sacral vertebrae were referred. At the same time Owen named three other species of Bothriospondylus. B. robustus was based on NHMUK R.22428, a dorsal from the same location. B. elongatus was based on a vertebra from Sussex, NHMUK R.2239, an original syntype of Ornithopsis hulkei. Finally, Bothriospondylus magnus was a new name for another syntype of Ornithopsis hulkei Seeley 1870, the present lectotype NHMUK 28632. Owen himself in an addendum to the same publication renamed B. robustus to Marmarospondylus robustus. Friedrich von Huene in 1908 referred the material to Pelorosaurus and in 1922 made B. suffossus into a Ornithopsis suffossa because the latter generic name has priority. More complete material from Madagascar was named by Richard Lydekker as a fifth species, Bothriospondylus madagascariensis. Franz Nopcsa in 1902 assigned to Bothriospondylus a vertebra from Argentina that later would be renamed Nopcsaspondylus. A skeleton from France was assigned to Bothriospondylus madagascariensis, but has been described as a new genus and species of brachiosaurid, Vouivria. In 1986 José Fernando Bonaparte moved material from "B." sp. into its own genus, Lapparentosaurus. The material, sometimes referred to B. madagascariensis, was separated into a few dorsal vertebrae to be the new lectotype of Lapparentosaurus. A revision in 2010 by Philip Mannion concluded that Bothriospondylus is a nomen dubium. However, "Bothriospondylus" madagascariensis was treated as valid and distinct from other Middle Jurassicsauropods from Madagascar.
Classification
Bothriospondylus has over the years been assigned to many groups — even in a Bothriospondylidae of its own — with Brachiosauridae lately being the most popular designation. However, the sparse and eroded material shows no synapomorphies of the Brachiosauridae and cannot be further determined than a very general Neosauropoda.
Current species
Only the type species of Bothriospondylus can be referred, because of the dubious nature of the genus.