Based on the well developed Isoetes sinensis plants material,with method of semi-thin section,we observed the development of the root and the characteristics of root system in detail,and discussed the endogenous origin of I.sinensis roots,the structural function of the thick roots and the fine roots the biological functioning of the dichotomous and transverse partition,which provided the morphologic basis for the study about ancient vascular plants evolution and their endangered reasons.The result show that:(1)The mature plants of I.sinensis have approximately one hundred brown,hollow roots,but have not main roots,both endogenous origin and external origin ways are observed among these roots,and each root has multi-round dichotomies.(2)The happened of dichotomies general frequency of intensive and fission unequality,among the thinner root are much more earlier and frequently and for every dichotomous point,there is a permanent transverse partition including 2-3 layers of cells between each inferior branch and its superior root.Even in the old root the transverse partition is always there.(3)The epidermis cells of inferior branches are transformed directly from some cortical cells;diameters of roots tips of these two inferior branches are different.These evidences suggested that:roots of I.sinensis could be originated from both stem and rhizophore;cortical cells have special differentiation capacity;the transverse partition may be a adaptive structure formed during the geological time million years ago,with what to against the high-energy environment in that era;root system of I.sinensis obtain powerful regenerative capacity and highly complicacy.