An anatomical profiling work on floral micromorphology of two critically endangered and endemic helmet orchids, Corybas selangorensis J.Dransf. & G.Sm. and Corybas holttumii J.Dransf. & G.Sm., was conducted. The objective of this study was to understand the diversity of the floral-surface micromorphology of the two species for the first time and their taxonomic significance. The micromorphology of the floral parts was observed using Scanning Electron Microscope (SEM); these were photographed, described, and illustrated. In the floral micromorphology of C. holtumii, there was an occurrence of anisocytic stoma which were observed on the dorsal sepal, and in contrast rare type holo-paracytic stomata which were observed on the dorsal sepal and bract of C. selangorensis. Sessile and long capitate glandular trichomes were observed on the dorsal sepal of C. holttumii, whereas neither glandular trichomes nor papillae were observed on C. selangorensis. Presence of stomata, glandular trichomes, and papillae on the dorsal sepal and labellum are the distinguishing characters. Trichomes and stomata offer more values on anatomical adaptions in defence and pollination for such species with inconspicuous habit rather than for release of fragrance. Different types of periclinal and anticlinal walls of the epicuticular ornamentation are useful to delimit and recognize the studied species from a similar subsection.