Faba bean (Viciafaba L.), one of the most important legumes in the world, evolved different types of cultivars due to its partial cross-pollination. The development of simple sequence repeat (SSR) markers from expressed sequence tags (EST) provided a useful tool for investigation of its genetic diversity. The purpose of the present study was to investigate the genetic diversity of faba bean from China and Europe using EST-SSR markers. 5 031 faba bean ESTs from the NCBI database were downloaded and assembled into 1148 unigenes. A total of 107 microsatellites in 96 unigenes were identified, indicating that merely 8.36% of sequences contained SSRs. The most abundant SSR within faba bean was tri-nucleotide repeat motif, and among all the tri-nucleotide repeats, the motif AAG/CTT was the most abundant type. Based on these results, 11 EST-SSR markers were used to assess the genetic diversity of 29 faba bean cultivars from China and Europe with two to three alleles per locus. The polymorphism information content value ranged from 0.0644 to 0.4278 with an average of 0.2919. Principal coordinate analysis (PCA) and phylogenetic clustering based on these 11 EST-SSR markers distinguished these cultivars into different groups. The results indicated that faba bean in China had a narrow genetic basis, and the additional sources of genetic cultivars/accessions should be introduced to enhance the genetic variability. The results of this study proved that the EST-SSR marker is very effective in evaluation of faba bean germplasm.