Firstly described as Sarcosiphon clandestinum by Blume (1849), and accepted as Sarcosiphon clandestinus by Schlechter (1921). Miquel (1859) transferred it to Thismia clandestina, which has been accepted by Jonker (1948) and Kiew (1999). It occurs on West Java, up to 1000 m above sea level.
A mistake ocurred in Janse (1896), who depicted a 'Thismia clandestina' without a mitra but having three long tepal appendages, which impossibly could have been T. clandestina (Blume) Miquel. Instead, the drawing of Smith (1910) in his description of Thismia javanica is remarkably close to the drawing in Janse (1896), who possibly worked on an yet undescribed specimen of T. javanica. Schlechter (1921), being aware of this confusion, synonymized 'Thismia clandestina Janse' with Thismia javanica J.J.Smith.