The phylogenetic position of extant tarsiers within the order Primates has been debated for much of the 20th century, and tarsiers have alternately been classified with strepsirrhine primates in the suborder Prosimii, or as the sister group to the simians (Anthropoidea) in the infraorder Haplorhini. Analysis of SINE insertions, a type of macromutation to the DNA, is argued to offer very persuasive evidence for the monophyly of Haplorhini, where other lines of evidence, such as DNA sequence data, remain ambiguous. Thus, some systematists argue the debate is conclusively settled in favor of a monophyletic Haplorrhini. In common with simians, tarsiers have a mutation in the L-gulonolactone oxidase (GULO) gene, which confers the need for vitamin C in the diet. Since the strepsirrhines do not have this mutation and have retained the ability to make vitamin C, the genetic trait that confers the need for it in the diet would tend to place tarsiers with haplorhines.
At a lower phylogenetic level, the tarsiers have, until recently, all been placed in the genus Tarsius, while it was debated whether the species should be placed in two (a Sulawesi and a Philippine-western group) or three separate genera (Sulawesi, Philippine and western groups).[13] Species level taxonomy is complex, with morphology often being of limited use compared to vocalizations.[citation needed] Further confusion existed over the validity of certain names. Among others, the widely used T. dianae has been shown to be a junior synonym of T. dentatus, and comparably, T. spectrum is now considered a junior synonym of T. tarsier.
In 2010, Colin Groves and Myron Shekelle suggested splitting the genus Tarsius into three genera, the Philippine tarsiers (genus Carlito), the western tarsiers (genus Cephalopachus), and the eastern tarsiers (genus Tarsius). This was based on differences in dentition, eye size, limb and hand length, tail tufts, tail sitting pads, the number of mammae, chromosome count, socioecology, vocalizations, and distribution. The senior taxon of the species, T. tarsier was restricted to the population of a Selayar island, which then required the resurrection of the defunct taxon T. fuscus.
In 2014, scientists from the University of the Philippines (Diliman Campus) – Institute of Biology in partnership with the University of Kansas have discovered a distinct genus of Philippine tarsier. The genetically distinct populations are found in the Dinagat Islands, Surigao del Norte, and probably Siargao Islands in Mindanao Island's northeast portion. Isolation is the key to the population's distinctiveness. Prior to the study, scientists generally accepted three subspecies of Philippine tarsier: the large island of Mindanao contained one subspecies, Tarsius syrichta carbonarius; while the islands of Samar and Leyte sported another, Tarsius syrichta syrichta; and Bohol held the third, Tarsius syrichta fraterculus. However the new genetic research found the relationships among the Philippine tarsier populations was even messier. Looking at mitochondrial and nuclear DNA, Brown's team uncovered three different evolutionary lineages: one lineage of tarsier makes their home on Bohol, Samar, and Leyte Islands (putting two presently accepted Philippine tarsier subspecies into a single subspecies); another has conquered the vast majority of Mindanao; while a long-cryptic branch has evolved in northeastern Mindanao and Dinagat Island (the new subspecies). For the purposes of the paper, the scientists refer to this as the Dinagat-Caraga tarsier. Rafe Brown of the University of Kansas' Biodiversity Institute, an author of the study, also said that through a more keen study, the only current Philippine tarsier species, Carlito syrichta, could be split into three distinct full species in the future.