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Prior to the advent of molecular work, the observable variation in vegetative reproduction has been used to classify <i>Lejeunea</i> into subgenera and sections. Thereby, the ability of developing caducous leaves was regarded as major factor. A reexamination of several <i>Lejeunea</i> specimens revealed that <i>L. cocoes</i> with caducous leaves shows considerable morphological differences with non-caducous leaved plants of <i>L. cocoes</i>. Phylogenetic analyses based on a three-marker dataset (<i>rbc</i>L, <i>trn</i>LF and the nuclear ribosomal ITS region) indicated two independent and robust lineages of the morpho-species <i>L. cocoes</i>. We consider both clades as two distinct species and therefore describe the new species, <i>L. malaysiana</i> for <i>L. cocoes</i> morpho-species with caducous leaves. <i>Lejeunea malaysiana</i> is characterized by its caducous leaves with ribbon-like and plantlet regenerants, strongly reduced leaf lobules, distant and deeply bilobed underleaves, long-keeled obovoid perianth, and autoicy and ranges from tropical Asia to the Pacific region.