To improve our knowledge of the woody flora of Cambodia, we collected specimens of trees, shrubs and woody vines within and near permanent plots of evergreen and deciduous tropical forests in lowland Cambodia. We sequenced rbcL and matK for most specimens, searched for species having high homologies with those sequences and then identified the collections using taxonomic literature and herbarium specimens. As a result, we identified 325 species in 69 families, including 163 trees, 90 shrubs, 67 vines, four palms and an epiphytic parasite. The frequencies of correct identification of BLAST searched sequences were low at the species level (about 15%), but high at the family and generic levels (about 100% and 75%, respectively). Twenty-one species were new to Cambodia. We corrected many previous misidentifications in the plot records.