Psilotum nudum a fern allies of the family Psilotaceae is found in two different habitats i.e. epiphyte and lithophyte. The present communication provided a comparative analysis of the anatomy and palynology between epiphytic and lithophytic habitats of P. nudum from Assam, India. Free hand transverse sections were made, following double staining technique, and permanent slides were prepared then examined under the microscopes. Scanning Electronic Microscopy (SEM) of the spores was conducted. The result shows similarity in the arrangement of cells in different vegetative parts in both habitats except minor differences in sizes. The presence of secondary metabolite i.e. phlobaphene in aerial stem is almost consistent, but the differences noted in its occurrence between the epiphytic and lithophytic rhizoids may reflect adaptive anatomical and chemical nature of the species. The spores are kidney shaped and similar in both habitats except minor differences in size. The study is expected to be useful to interpret the adaptive responses of epiphytic and lithophytic forms of P. nudum to different microhabitats.