Embodiments of the present application disclose a method and system for identifying whether an application is genuine by means of digital watermarks, which can conveniently determine whether an application is genuine. The method comprises: extracting a first digital watermark from an executable file of an application to be identified; using two decompiling-then-compiling algorithms on the executable file so as to generate, respectively, a first compilation file and a second compilation file having a same file format as that of the executable file, and extracting, respectively, a second digital watermark and a third digital watermark from the first compilation file and the second compilation file; acquiring, respectively, similarity between the first digital watermark and the second digital watermark and similarity between the first digital watermark and the third digital watermark; and if the similarity between the first digital watermark and the third digital watermark is higher than the similarity between the first digital watermark and the second digital watermark, determining that the application to be identified is genuine, otherwise, determining that the application to be identified is pirated. The present application is applicable to a scenario for identifying whether an application is genuine.