Use of the red seaweed Asparagopsis taxiformis as a feed additive for ruminant livestock dramatically reduces enteric methane emissions. The antimethanogenic effect of the seaweed is due to high content of halogenated bioactive compounds, primarily bromoform, which accumulate in specialised gland cells. These bioactives are synthesised by vanadium haloperoxidases (VHPOs) but the influence of specific VHPOs on bromoform concentration in A. taxiformis is unclear, as are the involvement of associated storage and transport genes. Understanding which genes contribute to bromoform production and storage will inform the development of bromoform-rich A. taxiformis strains to improve cultivation practices and scalability of the seaweed. Here, we investigated the effect of bromide availability for A. taxiformis to determine how gene expression and post-transcriptional regulation are influenced by decreased bromoform production. A. taxiformis (Sunshine Coast, Australia) was cultured in artificial seawater with either no bromide present or bromide added to the level in natural seawater. After 12 days in these conditions, microscopy confirmed the absence of gland cells in new growth from the bromide-free cultures. A transcriptomic approach incorporating differential gene expression and functional enrichment analyses highlighted upregulation of stress-related genes, including peroxidases and rhodophyte von Willebrand factor type A proteins. Furthermore, small RNA-seq was used to identify miRNA species with potential for post-transcriptional regulation of halogenation pathways. This research furthers our understanding of the molecular mechanisms underpinning bromoform biosynthesis for the development of a natural antimethanogenic feed additive.