Polypodiaceae is the second largest family of ferns characterized by creeping rhizomes covered with scales whose systematics however is mainly focused on frond and reproductive structures. Over the years, studies have demonstrated the significance of rhizome anatomical characters for fern taxonomy. However, work focusing on rhizome anatomy from the eastern Himalayan species is scanty. Morpho-anatomical characters of rhizome and rhizome scales of 30 fern species have been evaluated and compared for its taxonomic significance. Detailed observations were made using a light microscope (LM). Comparative micro-morphological and anatomical traits shared by close phylogenetically related species are also discussed. Anatomical traits like the presence and position of sclerenchymatic tissues, sclereids, thick lignified circumendodermal (CB) bands of vascular bundles, rhizome scales are taxonomically relevant. Characters of rhizome scale delimit several genera and are diagnostic for Polypodiaceae. The comparative rhizome anatomy helps us to better understand this fern family and the scale features outlined will aid in easy identification of several species. An artificial dichotomous key is constructed to discern the morpho-anatomical characters in the segregation of the examined species.