| Summary: | <i>Miscanthus sinensis</i> is an ornamental grass, non-food bioenergy crop, and forage with high feeding value. It can adapt to many kinds of soil conditions due to its high level of resistance to various abiotic stresses. However, a low level of seed germination restricts the utilization and application of <i>M. sinensis</i>. It is reported that the Homeodomain-leucine zipper (HD-Zip) gene family participates in plant growth and development and ability to cope with outside environment stresses, which may potentially regulate seed germination and stress resistance in <i>M. sinensis</i>. In this study, a complete overview of <i>M. sinensis HD-Zip</i> genes was conducted, including gene structure, conserved motifs, chromosomal distribution, and gene duplication patterns. A total of 169 members were identified, and the HD-Zip proteins were divided into four subgroups. Inter-chromosomal evolutionary analysis revealed that four pairs of tandem duplicate genes and 72 segmental duplications were detected, suggesting the possible role of gene replication events in the amplification of the <i>M. sinensis HD-Zip</i> gene family. There was an uneven distribution of <i>HD-Zip</i> genes on 19 chromosomes of <i>M. sinensis</i>. Also, evolutionary analysis showed that <i>M. sinensis HD-Zip</i> gene family members had more collinearity with monocotyledons and less with dicotyledons. The gene structure analysis showed that there were 93.5% of proteins with motif 1 and motif 4, while motif 10 was only found in group IV. Based on the cis-elements analysis, it appeared that most of the genes were related to plant growth and development, various hormones, and abiotic stress. Furthermore, qRT-PCR analysis showed that <i>Misin06G303300.1</i> was significantly expressed in seed germination and <i>Misin05G030000.1</i> and <i>Misin06G303300.1</i> were highly expressed under chromium, salt, and drought stress. Results in this study will provide a basis for further exploring the potential role of <i>HD-Zip</i> genes in stress responses and genetic improvement of <i>M. sinensis</i> seed germination.
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