Abstract: The bHLH proteins are the second large family of transcription factors,which play important roles in plant growth development,physiological metabolism and stress responses.In this study,Hippophae neurocarpa and H.tibetana were used as materials,the positive selection of the transcription factor bHLH94 gene was screened out using transcriptome sequencing.Based on the analysis of gene sequence and expression of HnbHLH94 and HtbHLH94,the response mechanism of bHLH94 gene in H.neurocarpa and H.tibetana adapted to altitude was studied.The HnbHLH94 and HtbHLH94 gene encoded 338 and 335 amino acids respectively.Sanger sequencing method verified the correctness of sequences,however there were 10 non-synonymous mutation sites outside the DNA binding domain of the two genes,which was speculated to be related to the adaptive evolution of the gene.As the altitude increased,the HnbHLH94 gene expression decreased,while the HtbHLH94 gene expression increased based on qRT-PCR technology.It suggested that gene might provide a molecular basis for adaptation to altitude,drought,freezing and radiation respectively,and the sequence structure and expression of HnbHLH94 and HtbHLH94 genes responded to the habitat conditions of elevation.