Abstract: WOX is a unique family of transcription factors in plants, which is mainly involved in the regulation of stem cell pluripotency, lateral organ development, flower organ formation and embryo development and other biological functions. Moreover, it is a kind of relatively old transcription factor, so there are also studies as a basis of evolutionary analysis. At present, WOX transcription factor family is found in most terrestrial and freshwater plants. In marine plants, there are few studies on this kind of transcription factors. Thalassia hemprichii is a common marine monocotyledonous plant in tropical areas with important ecological functions. In this paper, the wox transcription factor which belongs to the middle branch of WOX TF family, was screened using the transcriptome information of T. hemprichii obtained by high-throughput sequencing technology. The total length of CDS sequence is 597 bp and it encodes 198 amino acids. The three-dimensional structure of the transcription factor was modeled, which shows that it has typical HB structures. In the present study, we collected 93 WOX transcription factors located in the middle branch for homologous comparative analysis and phylogenetic tree analysis. The results showed that T. hemprichii had a close relationship with legumes and Ranunculaceae, which may indicate that T. hemprichii had evolutionary relationship between aquatic plants and terrestrial plants. As a kind of klysmoeionion,T. hemprichii is very important to balance the marine ecosystem. The in-depth study of the WOX transcription factor family gene of T. hemprichii will help us to further understand the genetic evolutionary relationship of T. hemprichii, and provide a theoretical basis for improving the artificial breeding of T. hemprichii.