Acuce, one of the rice landrace has being cultivated at Yuanyang Hani terrace more than one hundred years. For the purpose of intensively elucidating its population genetic characters under local rice production patterns, at present research, 24 populations were collected from local peasant household with stratified random sampling method. The intra- and inter- population of Acuce was analyzed through morphological traits and genetic diversity evaluation. The results showed that Acuce was classified into subspecies Oryzae indica, and displayed moderate resistance (MR) to Magnoporthe oryzae, the pathogenic fungi caused rice blast worldwide. Whatever intra- or inter-population, it showed blast resistance variation within all of the populations. For the reason of landrace harboring high frequent intra-heterogeneity, 30 single plants of each population were sampled and analyzed on 48 SSR loci which evenly distributed on 12 chromosomes of rice genome. The results showed that, whatever intra- or inter-population, 720 samples obtained 91 polymorphic alleles with polymorphic allele percentage 77.08%, and the mean of Nei diversity index 0.064 with the range 0-0.4302. Through cluster analysis, it indicated that genetic similarity coefficient range from 0.98-0.99 within 24 populations, and coefficient 0.86-1 between single plants within individual population. Taking Acuce source village as natural population, AMOVA results showed that it consisted of inter-village variation 3.36%, inter-population within village 33.15% and intra-village contributed 63.49% variation. Further, the cluster analysis result indicated that the inter-village genetic similarity correlated with geographical distance between villages.