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The hydrangea (<i>Hydrangea macrophylla</i> (Thunb). Ser.), an ornamental plant, has good marketing potential and is known for its capacity to change the colour of its inflorescence depending on the pH of the cultivation media. The molecular mechanisms causing these changes are still uncertain. In the present study, transcriptome and targeted metabolic profiling were used to identify molecular changes in the RNAome of hydrangea plants cultured at two different pH levels. De novo assembly yielded 186,477 unigenes. Transcriptomic datasets provided a comprehensive and systemic overview of the dynamic networks of the gene expression underlying flower colour formation in hydrangeas. Weighted analyses of gene co-expression network identified candidate genes and hub genes from the modules linked closely to the hyper accumulation of Al³⁺ during different stages of flower development. <i>F3′5′H</i>, <i>ANS</i>, <i>FLS</i>, <i>CHS</i>, <i>UA3GT</i>, <i>CHI</i>, <i>DFR</i>, and <i>F3H</i> were enhanced significantly in the modules. In addition, <i>MYB</i>, <i>bHLH</i>, <i>PAL6</i>, <i>PAL9</i>, and <i>WD40</i> were identified as hub genes. Thus, a hypothesis elucidating the colour change in the flowers of Al³⁺-treated plants was established. This study identified many potential key regulators of flower pigmentation, providing novel insights into the molecular networks in hydrangea flowers.