Upon their initial discovery, Jenkins and coauthors (2005) considered the Laotian rock rat to represent a completely new family. The discovery of a new species of an extant mammal genus happens periodically, such as with the leaf muntjac or saola. The discovery of a completely new family is, by comparison, much more unusual. The most recent incident before the discovery of the family Laonastidae by Western science was the discovery of the bumblebee bat (Craseonycteris thonglongyai; family Craseonycteridae) in 1974. The only other examples from the 20th century are species that are only considered distinct families by a few authorities. These discoveries are: the Chinese river dolphin (Lipotes vexillifer; family Lipotidae) in 1918, the Zagros mouse-like hamster (Calomyscus bailwardi; family Calomyscidae) in 1905, and Goeldi's marmoset (Callimico goeldii; family Callimiconidae) in 1904. Representatives from all the remaining rodent families with living representatives (approximately 30) were discovered before 1900.
Jenkins et al. (2004) did not compare the specimens to known rodent fossils. After such a comparison, Dawson et al. (2006) were of the opinion that the Laotian rock rat belongs to a previously described family which had only been known from fossils, the Diatomyidae. The Diatomyidae are known from a series of fossils from the early Oligocene (~32.5 mya) until the Miocene (~11 mya). The discovery of the Laotian rock rat means an 11 million-year gap exists in the fossil record where no diatomyids have been found. Dawson et al. (2006) described the Diatomyidae as a Lazarus taxon due to this gap. The only other mammal Lazarus taxon with a comparable time gap between it and its most recently known fossil relative is the monito del monte, which is part of a marsupial family (Microbiotheriidae) also most recently known from Miocene deposits. Mary Dawson described Laonastes as the "coelacanth of rodents".
The analysis of mtDNA 12S rRNA and cytochrome b sequence by Jenkins et al. (2004) allied Laonastes with African hystricognath rodents, namely the blesmols and the dassie rat. Support for such a placement was fair, but the exact position could not be resolved. Huchon et al. (2007) conducted a large-scale molecular phylogeny of rodents, including representatives of all major rodent taxonomic groups, based on 5.5 kb of sequence data from four nuclear and two mitochondrial genes, and a short, interspersed element, insertion analysis including 11 informative loci. Their molecular data place Laonastes robustly as a sister clade of Ctenodactylidae, and support an ancient divergence during the Lutetian (Early/Middle Eocene, ~44 mya). The earlier molecular study was in error due to long branch attraction and inadequate sampling.