The Phaeocystis globosa is a globally distributed harmful algal bloom species that causes serious damage to local environments and economies with each occurrence. The use of the invasive plant Ipomoea cairica as an algaecide for the P. globosa is an environmentally friendly management strategy. Although previous studies have found that I. cairica extracts can effectively inhibit the P. globosa growth, the molecular mechanism of cellular response to algaecide is not clear. Therefore, transcriptome differences between 24 and 48 h after treatment with I. cairica extracts were investigated to explore the P. globosa gene expression changes during algaecide.