Abstract: Tacca integrifolia is a tropical herb with a core distribution in southeast Asia and disjunct populations in the Brahmaputra valley in China. Significant morphological differences exist between the two regions. Genetic variation within and among four populations, three from the Brahmaputra valley, and one from Malaysia, was assessed using 19 Inter-Simple Sequence Repeat (ISSR) primers. The Malaysian population was more than 2,000 km from the other populations. A total of 165 discernible loci were obtained, of which 111 were polymorphic (67.68%). Genetic diversity was relatively high at the species level (PPB = 67.68%, H_T =0.185, and H_sp = 0.292), but was low within populations (PPB = 12.81%, H_E = 0.065 and H_pop = 0.044). Extremely high levels of population genetic differentiation were detected based on Nei’s genetic diversity analysis (G_ST = 0.777) and AMOVA analysis (F_ST =0.9206). Genetic differentiation among the three Brahmaputra populations (0.28%) and within these populations (7.94%) was low (P < 0.001). Restricted gene flow (N_m = 0.1435) among populations may result from self-pollination, inefficient seed dispersal, populationisolation, and habitat fragmentation. The extremely low genetic diversity in Brahmaputra populations was probably due to the unique landforms and vicariance of the Brahmaputra valley.