WRKY transcription factors are known to play important roles in the regulation of various aspects of plant growth and development, including germination, stress resistance, and senescence. Nevertheless, there is little information about the genes in Sieb. et Zucc., an important semimangrove plant. In this study, genes in were identificated based on Illumina RNA-sequencing and isoform sequencing from salt-treated roots. Then phylogenetic analysis and conserved motif analysis of the WRKY family in and were used to classify genes. Sixteen genes were selected from different groups to detect their expression patterns using real-time quantitative PCR in different organ (root, old leaf, tender leaf, receptacle, petal, or stamen) from 10-year-old plants grown in their natural environment and in seedlings with 8 to 10 true leaves challenged by phytohormone (salicylic acid, methyl jasmonate, or abscisic acid) and abiotic stress (drought, salt, or high temperature). As a result, the identified 78 genes were divided into two major groups and several subgroups based on their structural and phylogenetic features. Most transcripts of the selected 16 genes were more abundant in old than in tender leaves of . genes were regulated in reaction to abiotic stresses and phytohormone treatments and may participate in signaling networks to improve plant stress resistance. Some of genes behaved as would be predicted based on their homology with genes, but others showed divergent behavior. This systematic analysis lays the foundation for further identification of gene functions, with the aim of improving woody plants.