In plants, erucic acid is synthesized by the catalysis of a multienzyme complex, in which the the β- Ketoacyl-CoA synthase encoded by FAE1 (fatty acid elongase 1) is a key rate limiting factor. Erucic acid is mainly stored in seeds in the form of TAG and is an important oleochemical feedstocks. The FAE1 genes in plants are variable on DNA sequence, thus resulting in differences on capability of erucic acid synthesis. To identify and isolate FAE1 genes with the highest capability on erucic acid synthesis, four plant species including Brassica napus, Crambe abyssinica, Tropaeolum majus and Limnanthes douglasii were used and twelve encoded FAE1 sequences were obtained from their genomes by homologous cloning method. Each FAE1 gene was sub-cloned into the yeast expression vector, followed by the analysis of erucic acid content in each recombinant yeast under induction culture conditions. The results showed that the twelve FAE1 genes shared 52.1-99.9% and 49.9-99.8% identity on cDNA and amino acid sequence, respectively, showing species-specific characteristics. By GC-MS analysis of all recombinant yeasts, eight FAE1 genes derived from Mianyou328, Crambe abyssinica and Limnanthes douglasii have been demonstrated with the capability to synthesize very-long-chain fatty acids. CaFAE1-3 had the strongest capability to synthesize erucic acid (4.82%), followed by GjFAE1-1 (4.53%), and LdFAE1 that was the weakest one (0.29%). In addition, 95.39% of the C20:1 fatty acids were converted by CaFAE1-3, implying great application potential in high erucic acid breeding. The remaining four genes derived from Yangguang80 and Tropaeolum majus were not detected with the capability on erucic acid synthesis. This is possible because of GyFAE1-2, TmFAE1-1 and TmFAE1-2 that contain mutations in the conserved cysteine or (and) histidine sites, and GyFAE1-1 that contains a R395K mutation resulting in loss of enzyme activity. Collectively, this study represented better understanding of the relationship between the structure and function of FAE1 gene, which has implication in higher erucic acid breeding and genetic engineering improvement on erucic acid trait in rapeseed and Crambe abyssinica.