Many research results have indicated that many kinds of useful ingredients are rich in buckwheat, which have high nutritional values and medicinal properties, so, buckwheat has been cultivated around Asia and Europe. In this paper, genetic diversity of common and tartary buckwheat germplasms were studied based on morphological and molecular markers in order to provide useful information for conservation and utilization of buckwheat genetic resources. The length, width, thick, value and weight of the seed of the common and tartary buckwheat were measured and analyzed by the statistics methods. The result has shown that there are morphological variation both in common buckwheat and tartary buckwheat seeds collected from different regions. It also has shown that the morphological variation of tartary seeds was significantly correlated to geographical regions. The nuclear ribosomal internal transcribed spacers (ITS) of the tartary buckwheat collected from different countries were cloned, sequenced and statistically analyzed. The data showed that ITS sequences were informative to analyze the phylogeny of the tartary buckwheat and the data also showed that the genetic distances varied among different tartary buckwheat seeds collected from different countries.