<p><i>Nannochloropsis granulata</i> is a promising microalga for various biotechnological applications, including biodiesel feedstock production and aquaculture dietary supplements; it also serves as a source of digalactosyldiacylglycerols with potential anti-inflammatory properties. However, the absence of a species-specific genetic transformation system has substantially hindered the efforts to enhance its biotechnological potential. In this study, we developed a robust and efficient electroporation-mediated genetic transformation system for <i>N. granulata</i>. The strain used was isolated from Seonjaedo Island, Korea. Optimal concentrations of the antibiotics G418 and Zeocin were determined, and their corresponding resistance genes (<i>npt</i>II and <i>shble</i>) were utilized to select transgenic lines. Regulatory elements, including promoters and terminators of the <i>HSP70</i> and <i>UEP</i> genes from <i>Nannochloropsis salina</i>, were incorporated to drive the heterologous expression of transgenes. Functional validation was achieved through the expression of <i>sfCherry</i> as a live reporter gene for molecular studies of specific proteins and the use of biosynthetic genes for functional materials (e.g., mycosporine-like amino acids). Molecular analyses, including Southern blotting, Northern blotting, Western blotting, confocal microscopy, and high-performance liquid chromatography, confirmed stable integration and expression of transgenes in <i>N. granulata.</i> These results establish a reliable genetic transformation system for <i>N. granulata</i>, offering a valuable tool for routine genetic research while enabling further genetic improvement and exploitation of its biotechnological potential.</p>