National Botanical Garden of Iran (NBGI) includes endemic and exotic plants that besides a source of plant genetics, it is considered as a wealthy source for research and education of botany in Iran. The plant parasitic nematodes in some collections including Hyrcanian habitat, Zagros habitat and Medicinal and aromatic garden were studied by collecting soil and root samples from trees, shrubs and annual plants. The nematodes were identified based on morphological and morphometric characters and based on these characters 34 species belonging to 19 genera were identified. Pratylenchus spp. with four species, followed by Helicotylenchus, Meloidogyne and Paratylenchus each one with three species were the more frequent genera. The species of Tylenchidae family showed higher frequency and multiplicity in Medicinal and aromatic collection. Due to infection of Brant’ s oak (Quercus brantii Lindl. ), oak manna (Q. infectoria Oliv. ), Pistacia atlantica and a few of medicinal plants to some species of plant parasitic nematodes i. e. Root Knot Nematodes, Root Lesion Nematodes, Ring and Dagger Nematodes, establishment of new plots with the seedlings free from the plant parasitic nematodes is emphasised. CEPHALENCHUS daisuce, Coslenchus capsici from Hyrcanian habitat and Paratylenchus ciccaronei from Medicinal and aromatic garden are new records from Iran.