Using genome-wide SNP data obtained from high-throughput techniques based on a double digest restriction site-associated DNA sequencing (ddRAD-seq), we elucidated the migration history and genetic diversity of the ecologically important red seaweed Gelidium elegans Kuätzing in Japan. STRUCTURE and NeighborNet analyses showed a clear genetic differentiation among three geographic regions: Sea of Japan and Pacific coast of Tohoku region (POP1), Mie and Kochi (POP2), and Shizuoka and Chiba (POP3). Approximate Bayesian Computation (ABC) analysis indicated that POP1 diverged first, followed by a separation of remaining populations into POP2 and POP3. Low genetic diversity was detected in POP1, whereas high genetic diversity was detected in POP2 and POP3.