Repeated column separation yielded four enterolactone type lignans from Forsythia koreana flowers (FKF), whose chemical structures were identified using several spectral technics. FKF MeOH extract (FKFM) and four lignans significantly recovered aloxan induced pancreatic islet in zebrafish. Especially, aglycones, 1 and 3, exhibited relatively higher activity than the lignan glycosides, 2 and 4. Therefore, FKFM was fermented using a Microbacterium esteraromaticum, BGP1, to yield the fermented FKFM (FKFM-BGP1). FKFM and FKFM-BGP1 were extracted using n-butanol to give n-BuOH fraction of each, FKFM-nB and FKFM-BGP1-nB, respectively. FKFM-BGP1-nB showed higher activity than FKFM-nB, as well the content of the aglycones, 1 and 3, in FKFM-BGP1-nB, 2.42 ± 0.01% and 1.15 ± 0.01%, was revealed to be much higher than that in FKFM-nB, 0.01 ± 0.01% and 0.01 ± 0.01%, respectively. In conclusion, the lignan aglycones 1 and 3 as well FKFM-BGP1-nB from F. koreana flowers were proved to be potential anti-diabetic agents. Furthermore, we suggest that antidiabetic efficacy of FKFM-BGP1-nB might be related to lignan aglycones 1 and 3.