The tropical seagrass Halophila stipulacea invaded the Eastern Mediterranean Sea in the late nineteenth century and progressively spread throughout the basin ever since. Its spread is expected to continue north-westward as the Mediterranean Sea becomes warmer, potentially changing the seagrass biogeography of the basin. Given the power of genomics to assess invasion dynamics in non-model species, we report the first ddRAD-seq study of H. stipulacea and small-scale population genomic analysis addressing its century-old Mediterranean invasion. Based on 868 SNPs and 35 genotyped native (Red Sea) and exotic (from Cyprus, Greece, and Italy) samples, results suggest that genetic structure was high, especially between major geographic discontinuities, and that exotic populations maintain comparably lower genetic diversity than native populations, despite 130 years of invasion. The evidence of high heterozygosity excess, coupled with previously reported male-dominated and rare flowering records in the exotic range, suggests that clonal propagation likely played a pivotal role in the successful colonization and spread of H. stipulacea in the Mediterranean. This shift in reproductive strategy, particularly evident in the Italian populations located closest to the western boundary and representing more recent establishments, underscores the importance of this cost-effective mode of reproduction, especially during the initial stages of invasion, raising questions about the species future expansion trajectory. Our findings serve as a catalyst for future research into the species’ invasion dynamics, including deciphering the intricate roles of acclimatization and rapid adaptation, important for a comprehensive assessment of invasion risks and improving management strategies aimed at conserving seagrass ecosystems.