Landraces are important genetic resources for future rice improvement. Even though genetic variability in rice landraces make it difficult to identify them, accurate identification is necessary for collecting rice landrace to genetic conservation and using landraces as agermplasm resource. In this study, we assessed seed morphology and leaf and lemma surface character state of Bue Po Lo rice in Mae Hong Son province, northern Thailand. Approximately 100 seeds from each farmer’s field were collected and germinated and then the 15 intact seedling of each field were selected for the study. All plants at the flowering stage were recorded their general morphology. Epidermal anatomy of the lemmas and leaves were determined using both stereo microscope and light compound microscope. After harvest, the seed length and width, color, lemma surface were studied. A great diversity in grain shape, grain color, apiculus color, lemma surface and leaf surface justified dividing Bue Po Lo rice into 14 groups. The Shannon’s indices of each of the samples were lower than that of all samples taken together. The differences in stomatal index of the upper epidermis of each group may affect variation of each group’s physiology. The encountered high diversity of Bue Po Lo rice may benefit the plants and secure their survival under natural disturbance.