The Highlands controversy was a scientific controversy which started between British geologists in the middle of the nineteenth century concerning the nature of the rock strata in the Northwest Highlands of Scotland. The disagreement stemmed from the apparent ages of the strata, particularly the existence, now confirmed, of older rock above younger rock as well as duplicated and inverted strata, which could not be satisfactorily explained by contemporary geology. This rock formation and surrounding controversy were the impetus for Albert Heim's theory of thrust faulting, which, in conjunction with anticlines and imbrication, are now commonly accepted as the primary geological mechanisms that created the Northwest Highlands rock strata.

At the time, the debate became contentious, even acrimonious, because of some of the personalities involved and because it pitted professional geologists of the Geological Survey against academic and amateur geologists. An initial resolution was achieved by about 1886 but the great complexity and scientific importance of the discovery of the Moine Thrust Belt and the geological processes involved in its creation led to field work continuing for a further twenty years culminating in the 1907 publication by the Geological Survey of a book of fundamental geological significance: The Geological Structure of the North-West Highlands of Scotland.

The acrimony was an important factor in the political decision to set up the Wharton Committee of 1899 to review the state-funded Geological Survey. The committee's report probably precipitated the retiral of Archibald Geikie, the Survey's director-general, who had been slow to accept the new geological paradigm. However, in retirement Geikie's status flourished as he went on to become president both of the Geological Society and the Royal Society and to receive the Order of Merit.

The northwest highlands region of Scotland is now known to be where part of the Iapetus Ocean closed with the collision of the continents of Laurentia and Baltica about 400 million years ago. The consequent Caledonian Orogeny produced intense folding and compression of rocks – at thrust faults older rock strata slid for miles over younger rocks and, at nappes, the sequences of rock strata became inverted and duplicated at overturned anticlines.

From around 1830 geologists were beginning to date rocks according to the embedded fossils. The law of superposition whereby younger rocks lie above older ones was very well established and it was recognised that some layers may be missing because they had been eroded away. Folding and faulting of strata were recognised and in 1841 Arnold Escher von der Linth discovered that sometimes older rocks lay above younger ones. However his explanation involved such large horizontal movements of rock and folding on such a massive scale that he was afraid to publish his results because his theory would seem ridiculous. It was not until after his death that his pupil Albert Heim published the findings in 1878. Thrust faulting, where there is a considerable horizontal movement of younger strata over older, had not yet been identified.

Roderick Murchison's expedition to Wales in 1831 led to his identification of the Silurian period and he came to regard the Silurian geological system as being his own territory. He went on to decide that Silurian rocks extended into parts of England and southern Scotland and this caused bitter arguments with his friend Adam Sedgwick who had previously identified the rocks as Cambrian − the intervening Ordovician period was yet to be characterised. Murchison identified the Silurian on the basis of the types of fossils the rocks contained whereas earlier geologists had studied the type of rock. The strength of Murchison's views became buttressed by his knighthood in 1846 and when he was appointed director-general of the Geological Survey in 1855 he decided to turn his researches to the little-known and even less understood Northwest Highlands of Scotland expecting to extend his Silurian domain up there.

The Northwest Highlands were, and still are, remote and difficult to access. Along a coastal strip some 200 kilometres (120 mi) long and 15–25 kilometres (10–15 mi) wide the terrain is austere with isolated mountains rising above barren lower ground where knolls of bare rock lie among lochans and peat bogs. This geological region runs from the Sleat peninsula of Skye northward through Kyle of Lochalsh, Ullapool and Assynt to Cape Wrath and Loch Eriboll.

For the geologist Assynt provides some of the best formations of rock and the finest scenery. The low-lying hummocky ground to the west is of hard metamorphic rock – Lewisian gneiss, the oldest rock in Britain. Above this basement are less-disturbed sandstones, quartzite and some Durness limestone. No fossils are to be found in the sandstone; the quartzite contained "Pipe Rock" but at the time this was not recognised as containing fossils; and the fossils in the limestone could not be unambiguously dated at the time. Away to the east of the coastal strip are the strongly metamorphosed Moine rocks which in places lie above non-metamorphosed strata.