<p>The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas system is a powerful tool for gene editing, yet it has never been successfully applied to edit genes in dinoflagellates. In CRISPR-Cas-mediated gene editing, magnesium ions (Mg²⁺) are necessary to maintain catalytic activity. Some studies, however, found that Mg²⁺ and calcium (Ca²⁺) ions could modulate flagellar motility and cyst formation of unicellular flagellates, thus affecting their physiology. Here, a single-cell microinjection method was adapted to deliver Mg²⁺/Ca²⁺ into cells of the dinoflagellate <i>Alexandrium catenella</i> to test the dose-dependent effects on cyst formation and germination. It was found that Mg²⁺/Ca²⁺ treatments ≤50 mmol/L significantly enhanced cyst survival and germination rates on day 1 compared to those of higher concentrations. In contrast, treatments with high concentrations (≤250 mmol/L) of Mg²⁺/Ca²⁺ triggered irreversible dormancy transitions, accompanied by increased mortality and prolonged germination time. The treatment with 10-mmol/L Mg²⁺ achieved an optimal balance between CRISPR-Cas nuclease activity and cyst germination. This work provides the first experimental assessment of ion, induced cyst physiology using single-cell microinjection in dinoflagellates, and identifies Mg²⁺ concentrations that are physiologically compatible with microinjection. These findings establish the fundamental conditions for future microinjection-based CRISPR delivery in <i>A. catenella</i>.</p>