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Background   Lonicera japonica  Thunb. flower has been used for the treatment of various diseases for a long time and attracted many studies on its potential effects. Transcription factors (TFs) regulate extensive biological processes during plant development. As the restricted reports of  L. japonica  on TFs, our work was carried out to better understand the TFs’ regulatory roles under different developmental stages in  L. japonica .    Results  In this study, 1316 TFs belonging to 52 families were identified from the transcriptomic data, and corresponding expression profiles during the  L. japonica  flower development were comprehensively analyzed. 917 (69.68%) TFs were differentially expressed. TFs in bHLH, ERF, MYB, bZIP, and NAC families exhibited obviously altered expression during flower growth. Based on the analysis of differentially expressed TFs (DETFs), TFs in MYB, WRKY, NAC and LSD families that involved in phenylpropanoids biosynthesis, senescence processes and antioxidant activity were detected. The expression of  MYB114  exhibited a positive correlation with the contents of luteoloside; Positive correlation was observed among the expression of  MYC12 ,  chalcone synthase (CHS)  and  flavonol synthase (FLS) , while negative correlation was observed between the expression of  MYB44  and the synthases; The expression of  LSD1  was highly correlated with the expression of  SOD  and the total antioxidant capacity, while the expression of  LOL1  and  LOL2  exhibited a negative correlation with them; Many TFs in NAC and WRKY families may be potentially involved in the senescence process regulated by hormones and reactive oxygen species (ROS). The expression of  NAC19 ,  NAC29 , and  NAC53  exhibited a positive correlation with the contents of ABA and H 2 O 2 , while the expression of  WRKY53 ,  WRKY54 , and  WRKY70  exhibited a negative correlation with the contents of JA, SA and ABA.    Conclusions  Our study provided a comprehensive characterization of the expression profiles of TFs during the developmental stages of  L. japonica . In addition, we detected the key TFs that may play significant roles in controlling active components biosynthesis, antioxidant activity and flower senescence in  L. japonica , thereby providing valuable insights into the molecular networks underlying  L. japonica  flower development.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1803-1) contains supplementary material, which is available to authorized users.

Transcriptional regulation of Lonicera japonica Thunb. during flower development as revealed by comprehensive analysis of transcription factors