AbstractTo explore the differences between the hypericum in the Changbai Mountains, we carried out a transcriptome analysis of two common hypericums in the area, which wasHypericum attenuatumChoisy andHypericum longistylumOliv. We screened theMADS‐boxgenes to analyze divergence time and evolutionary selection expression, and determine their expression levels. The results showed that we detected 9287 differentially expressed genes in the two species, of which shared 6044 genes by the two species. Analysis of the selectedMADSgenes revealed that the species was in an environment adapted to its natural evolution. The divergence time estimation showed that the segregation of these genes in the two species was related to the changes of external environment and genome replication events. The results of relative expression showed that the later flowering period ofHypericum attenuatumChoisy was related to the higher expression of theSVP (SHORT VEGETATIVE PHASE)and theAGL12 (AGAMOUS LIKE 12), while the lower expression of theFUL (FRUITFULL).