Using microsatellite markers for analyzing genetic diversity of native brown planthopper resistance rice varieties in Vietnam showed that: these native brown planthopper resistance rice varieties have diversity about allele components. The results using 31 SSR markers for analyzing genetic diversity of native brown planthopper resistance rice varieties have obtained a total number of 1,062 DNA bands belong to 119 differences allele (with a mean of 3.84 alleleper locus). PIC value changed from 0.11 to 0.86 (with a mean of 0.59). The ratio of homozygosity of native brown planthopper resistance rice varieties changed from 0 to 3.6 percent. Genetic similarity coefficients of 35 native brown plant hopper resistance rice varieties were ranging from 0.15 to 0.82. Genetic similarity was determined using Jaccard's similarity coefficients and final dedrogram construction using a UPGMA clustering methods showed that 35 varieties were divided into five major groups. This result is very useful to classify, define heterotic groups, selection of gene resources and brown planthopper resistance rice breeding.