Background/Objectives: Biogenic volatile organic compounds (BVOCs), extensively studied in terrestrial plants with global emissions around 1 PgC yr−1, are also produced by marine organisms. However, benthic species, especially seagrasses, are understudied despite their global distribution (177,000–600,000 km2). This study aims to examine BVOC emissions from key Mediterranean seagrass species (Cymodocea nodosa, Posidonia oceanica, Zostera noltei, and Zostera marina) in marine and coastal lagoon environments. Methods: BVOCs were collected using headspace solid-phase microextraction (HS-SPME) using divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS) fibers and analyzed by gas chromatography–mass spectrometry (GC-MS). Results: An important chemical diversity was found with a total of 92 volatile compounds (61 for Z. noltei, 59 for C. nodosa, 55 for P. oceanica, and 51 for Z. marina), from different biosynthetic pathways (e.g., terpenoids, benzenoids, and fatty acid derivatives) and with several types of chemical functions (e.g., alkanes, esters, aldehydes, and ketones) or heteroatoms (e.g., sulfur). No differences in chemical richness or diversity of compounds were observed between species. The four species shared 29 compounds enabling us to establish a specific chemical footprint for Mediterranean marine plants, including compounds like benzaldehyde, benzeneacetaldehyde, 8-heptadecene, heneicosane, heptadecane, nonadecane, octadecane, pentadecane, tetradecane, and tridecanal. PLS-DA and Heatmap show that the four species presented significantly different chemical profiles. The major compounds per species in relative abundance were isopropyl myristate for C. nodosa (25.6%), DMS for P. oceanica (39.3%), pentadecane for Z. marina (42.9%), and heptadecane for Z. noltei (46%). Conclusions: These results highlight the potential of BVOCs’ emission from seagrass ecosystems and reveal species-specific chemical markers.