Phytohormones, such as auxins and cytokinins, take part in the integration of growth control and stress response, but their role in algal adaptation to heavy metal remains to be elucidated. The current research indicated that lead (Pb), one of the most toxic metals in nature, causes severe depletion of endogenous cytokinins, auxins, and gibberellin and an increase in abscisic acid content in the green alga Acutodesmus obliquus. Exogenous auxins and cytokinins alleviate Pb toxicity through the regulation of the endogenous phytohormones' levels. Exogenously applied auxins provoked the coordinated activation metal tolerance mechanisms leading to the increase in phytochelatin synthase activity and accumulation of phytochelatins and their precursors, which are essential for Pb sequestration. On the other hand, phytochelatin synthesis decreased in algal cells treated with cytokinins. Significant changes in the levels of low molecular weight metabolites, mainly involved in metal chelation and glutathione synthesis pathway under the influence of phytohormones in algal cells growing in the presence of Pb stress, were observed. This is the first report showing that auxins and cytokinins are important regulatory factors in algal adaptation strategies to heavy metal stress based on thiol-mediated compounds and the maintenance of phytohormone homeostasis.