Monochoria C. Presl is a genus member of the aquatic plant family Pontederiaceae which exhibits high morphological variations. The populations of Monochoria vaginalis exhibit extreme variations in their morphology. Previous morphological and phenetic studies suggested that M. vaginalis s.l. in Thailand contained cryptic species. In this recent study, the molecular data from DNA sequencing and phylogenetic analysis of 50 living plants from 10 populations of M. vaginalis with 3 outgroups using 5 regions from both cpDNA and nuclear DNA were intensely investigated. The results showed a similar trend as in previous studies that M. vaginalis populations should be separated into 2 species. The new species, M. angustifolia (G. X. Wang) Boonkerd & Tungmunnithum, is also described in this work.