<p><i>Hippeastrum</i> species and their hybrids, valued for their vibrant flowers and ease of cultivation, are significant in the ornamental industry. This study employed <i>de novo</i> transcriptome analysis to investigate the molecular basis of floral color and fragrance in <i>Hippeastrum brasilianum</i>, <i>Hippeastrum papilio,</i> and their F₁ hybrid. A high-quality transcriptome was assembled from 637,934,284 paired-end reads, resulting in 557,833 high-confidence transcripts. BUSCO analysis confirmed the completeness of the assembly, with 94.5% of eukaryotic, 88.1% of monocot, and 90.7% of land plant genes identified as complete. Differential gene expression analysis revealed that the genes involved in monoterpene, diterpenoid, and sesquiterpenoid biosynthesis were upregulated in <i>H. brasilianum</i>, contributing to its distinct fragrance profile, while their downregulation in <i>H. papilio</i> and their hybrid suggests a loss of scent, consistent with previous fragrance analyses in <i>Hippeastrum</i> species. The upregulation of flavonoid and phenylpropanoid biosynthesis genes in <i>H. papilio</i> and their hybrid enhanced anthocyanin production, leading to vibrant pigmentation, whereas <i>H. brasilianum</i> showed reduced expression, aligning with its white flowers. Gene Ontology (GO) and EuKaryotic Orthologous Groups (KOG) classifications highlighted the prominence of metabolic and cellular processes, supporting their roles in floral trait development. These findings provide a molecular framework for understanding floral trait variation in <i>Hippeastrum</i>, offering insights for breeding programs aimed at enhancing ornamental qualities.</p>