A new species belonging to the mycoheterotrophic genus Thismia is described and illustrated. Thismia inconspicua was found in a lowland mixed dipterocarp forest in Ulu Temburong National Park, Brunei Darussalam. It is characterized by its sepia-brown perianth with free equal lobes with very short terminal appendages, two pairs of appendages on connective apices, perianth tube displaced from the ovary axis and short stem. DNA sequence data from commonly studied nuclear and mitochondrial loci are provided. Phylogenetic analysis confirmed the close relationship with other members of section Thismia, subsection Odoardoa. An updated determination key of Thismia species of Borneo is included.