Abstract: The experiment took 90 SSR markers to analyze the genetic relationship among 17 flax cultivars. Although SSR markers have the advantages of high efficiency and specificity, which still got less application on flax currently. In this study, 90 SSR markers that evenly distributed on different flax chromosome were screened for polymorphism analysis. The result showed that clear and stable polymorphic bands were amplified for all of the tested SSR primers. A total of 170 different amplification bands were detected. 17 flax cultivars were divided into 5 groups, among them '9801-1-17' and 'Akata' had the largest genetic distance. The second group and the fifth group had only one species, which were 'A29' and '9801-1-17' respectively. They were far away from other cultivars in genetic relationship. This research showed that SSR technology should be widely utilized on the flax breeding for high accuracy and efficiency. The cultivars with distant genetic relationship can be used for hybridization breeding and further genetic analysis on agronomic traits.