The Java mouse-deer's common scientific name is "Tragulus javanicus", although other classification names for it exist, including "Tragulus javanica", "Cervus javanicus", and the heterotypic synonym "Tragulus fuscatus". The Java mouse-deer is also known by many common names, including Javan chevrotain, Javan mousdeer, or Java Mousedeer. The taxonomic status of the Java mouse-deer is questionable, but recent craniometric analyses have begun to shed light on the taxonomic discrepancies. Previously, the Java mouse-deer, "Tragulus javanicus", was commonly thought to represent the wider class of large chevrotains, but it was found that these, unlike the Java mouse-deer, do not likely reside on Java. Three species groups 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). Thus, because of its uniqueness 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.