The phylogenetic and taxonomic delimitation of Cleome L. species in southwest Asia has not been sufficiently investigated, and there are still unresolved taxonomic issues. In order to shed light on the use of micromorphological and morphological traits in the taxonomic delimitation of these Cleome species, phylogenetic analyses were conducted based on nucleotide sequences in the rDNA ITS region. Bayesian, maximum parsimony, and maximum likelihood analyses were performed, yielding trees with similar topology. The results revealed two main clades (Cleome s.s. and Rorida J.F. Gmel.) and three lineages (Khorassanica, Ornithopoides and Coluteoides), some of which incongruent with previous sectional subclassification. High resolution light and Scanning Electron Microscope (SEM) photographs of micromorphological and morphological characteristics of Cleome and Rorida flowers, pollen grains, fruits and seeds were also provided. Almost all of the studied characters, which hold taxonomic significance, corresponded to the phylogenetic groups and are documented in this study. As a result, three new sections were generated to distinguish southwest Asian Cleome species into distinct lineages.