Described by Smith (1910), accepted by Jonker (1948) and Larsen (1987). Subsequent to the taxonomic description of Smith, Bernard and Ernst (1910a) have provided a detailed anatomical characterization, as well as studies on embryology (Bernard and Ernst 1910b). According to Jonker (1948) T. javanica is very close to Thismia arachnites, and might be conspecific. It occurs in Sumatra and Java as well as in southwest Thailand (Ranong). More recently it was also found in Malaysia,Terengganu, Kuala Berang District, Hulu Telemong Forest Reserve (Siti-Munirah and Dome 2019).
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.