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The Java mouse-deer's current scientific name is ''Tragulus javanicus'', although other names for it exist, including ''Tragulus javanica'' ([[Feminine sense|fem.]]), ''Cervus javanicus'' ([[basionym]]), and ''Tragulus fuscatus'' ([[heterotypic synonym]]).<ref name="iucn status 12 November 2021" /><ref name=meijaard>{{cite journal | last1 = Meijaard | first1 = I. | last2 = Groves | first2 = C. P. | year = 2004 | title = A taxonomic revision of the Tragulus mouse-deer. | journal = Zoological Journal of the Linnean Society | volume = 140 | pages = 63–102 | doi=10.1111/j.1096-3642.2004.00091.x| doi-access = free }}</ref><ref name=ARKive4>Javan mouse-deer (Tragulus javanicus). (2013). ARKive - Discover the world's most endangered species. Retrieved from http://www.arkive.org/javan-mouse-deer/tragulus-javanicus {{Webarchive|url=https://web.archive.org/web/20131207213548/http://www.arkive.org/javan-mouse-deer/tragulus-javanicus/ |date=2013-12-07 }}</ref><ref>Facts about Lesser Mouse Deer (Tragulus javanicus) - Encyclopedia of Life. (n.d.). Encyclopedia of Life - Animals - Plants - Pictures & Information. Retrieved from http://eol.org/pages/328339/names/synonyms</ref>
The taxonomic history of the Java mouse-deer is convoluted; previously, the Java mouse-deer (''Tragulus javanicus'') was commonly thought to encompass a group of small-bodied [[chevrotain]]s, but after revisions it was found that this species name should only apply to mouse-deer specimens from [[Java]].<ref>{{cite journal |last1=Stone |first1=Witmer |last2=Rehn |first2=J. A. G. |title=A Collection of Mammals from Sumatra, with a Review of the Genera Nycticebus and Tragulus |journal=Proceedings of the Academy of Natural Sciences of Philadelphia |date=Jan–Apr 1902 |volume=54 |issue=1 |pages=127–132 |jstor=4062829 |url=https://www.jstor.org/stable/4062829?seq=10 |access-date=4 June 2025}}</ref>
Recent [[Craniometry|craniometric]] analyses have begun to shed light on the taxonomic discrepancies. Three [[species group]]s of ''Tragulus'' have been identified based on craniometric skull analyses and coat coloration patterns. These three species groups are ''Tragulus javanicus'', ''[[Tragulus napu]]'', and ''[[Tragulus versicolor]]''. Based upon these craniometric analyses, ''Tragulus javanicus'' was then further separated based on the organisms’ known geographic locations: ''[[Tragulus williamsoni]]'' (found in northern Thailand and possibly southern China), ''[[Tragulus kanchil]]'' (found in Borneo, Sumatra, the Thai–Malay Peninsula, islands within the Greater Sunda region, and continental Southeast Asia), and ''Tragulus javanicus'' (found in Java).<ref name=meijaard6>{{cite journal | last1 = Meijaard | first1 = E. | last2 = Groves | first2 = C. P. | year = 2004 | title = A Taxonomic Revision Of The Tragulus Mouse-deer (Artiodactyla) | journal = Zoological Journal of the Linnean Society | volume = 140 | issue = 1| pages = 63–102 | doi=10.1111/j.1096-3642.2004.00091.x| doi-access = free }}</ref> Thus, because of its [[endemism]] to the island of Java, the Java mouse-deer is now considered a distinct species, although this fact has not significantly affected its current classification.{{Clarify|date=June 2025}}<ref name=redorbit7>Java Mouse Deer, ''Tragulus javanicus'' - Mammals Reference Library - redOrbit. (n.d.). redOrbit - Science, Space, Technology, Health News and Information. Retrieved from http://www.redorbit.com/education/reference_library/science_1/mammalia/1112721404/java-mouse-deer-tragulus-javanicus/</ref>
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