Abstract: To investigate the molecular and physiological mechanisms underlying adventitious bud induction during in vitro leaf regeneration and clonal propagation of the endangered medicinal mangrove species Acanthus ebracteatus Vahl., three leaf-derived materials were analyzed: intact leaf blades (Ae_W), leaves with only adventitious roots (Ae_G), and leaves with only regenerated leaves (Ae_Y). Full-length transcriptome sequencing was integrated with short-read RNA sequencing and LC-MS/MS-based hormone metabolomics to characterize transcriptional and hormonal changes associated with organ differentiation. Full-length transcriptome sequencing generated 46 353 transcripts, with an average length of 3 466 bp. Hormone profiling detected 49 phytohormone-related metabolites, 11 of which differed significantly among developmental states. BAP content was highest in Ae_Y, ABA-GE was detected only in Ae_G, and free IAA was present exclusively in Ae_W, indicating dynamic hormonal regulation during organ differentiation. Compared with Ae_W, Ae_Y and Ae_G contained 622 and 502 differentially expressed genes (DEGs), respectively, with enrichment in "metabolic pathways" and "biosynthesis of secondary metabolites". Integrated transcriptomic and metabolomic analysis revealed marked activation of auxin signaling genes (AUX1, TIR1, AUX/IAA, ARF, GH3, and SAUR) in Ae_Y, together with increased expression of ABA signaling genes encoding PYR/PYL receptors, PP2C phosphatases, and ABF transcription factors. These patterns suggest that coordinated auxin and ABA signaling contributes to adventitious shoot formation during leaf regeneration. qRT-PCR validation of eight key DEGs confirmed the RNA-seq expression trends. These findings provide mechanistic insight into hormone-regulated vegetative propagation in A. ebracteatus and offer a molecular basis for improving regeneration systems and supporting germplasm conservation and sustainable use.