Monochoria C. Presl, an extreme morphological variable genus, belongs to an aquatic plant family, Pontederiaceae. According to the Flora of Thailand, there are 3 monotypic species, i.e. M. elata Ridl., M. hastata (L.) Solms and M. vaginalis (Burm.f.) C. Presl ex Kunth. Previously, their morphological plasticity led to ambiguous identification and classification of the species members. This research was designed to clarify taxonomic status and species boundary of the genus. Morphological, phenetic, anatomical, palynological, chromosome and phylogenetic studies were carried out on 25 Monochoria’s populations The morphological study showed high morphological variations among the studied populations. The variation in leaf base, groove on petioles and peduncles, inflorescence type, number of flowers per inflorescence, shape of inner perianth, seed shape and longitudinal ridges on seed surface provided important criteria for dividing the 25 Monochoria’s populations into 5 forms, i.e. morphological form I, II, III, IV and V. Likewise, cluster and canonical discriminant analyses in phenetic study pointed out that the 25 studied populations could be divided into 5 groups, which correspond with the morphological form I-V based on lamina width of floral-leaf, petiole length of floral-leaf and flowering stem length. Phylogenetic study using 5 regions from cpDNA and nuclear DNA classified the Thai Monochoria into 4 major clades, with one clade subdivided into 2 minor clades. This result was also in agreement with the morphological and phenetic studies. The equal and different number of chromosome was also useful in delimiting species in the Monochoria. However, the examined characters in the anatomical and palynological studies are not suitable to use as the diagnostic characters for the Monochoria’s classification. To sum up, the results from morphological, phenetic, and genetic diversity studies indicated that the Thai Monochoria contained cryptic taxa, which consists of 4 species and 2 subspecies: M. vaginalis sensu stricto and a new treated species, M. siamensis ined., M. elata Ridl. subsp. elata and M. elata Ridl. subsp. valida ined., a new treated subspecies and a homogeneous species, M. hastata.