Seagrasses represent the unique re-colonization of the marine ecosystem by angiosperms. As their terrestrial relatives, seagrasses are important habitat providers but in contrast, their microbiomes are still poorly known. The microbial community associated with terrestrial plants is intensively studied and plays an important role in plant fitness. The close relation of seagrasses to terrestrial plants suggests a resemblance in survival strategies, including the creation of a microbiome distinct of the surrounding environment. To obtain more knowledge regarding seagrass microbiomes and their intra- and interspecies differentiation, samples of three tropical seagrass species occurring around the island of Curaçao, the invasive Halophila stipulacea and the natives Halodule wrightii and Thalassia testudinum, were collected. Root and leaf-associated microbes were separately analyzed using high throughput Illumina sequencing of the region V5-V7 of the 16S rRNA gene. Sequences were aligned and clustered into Operational Taxonomic Units (OTUs). Results displayed the occurrence of a seagrass-specific microbiome, distinct from that of the surrounding seawater and sediment. The existence of a species and tissue (root/leaf) specific bacterial community and structure was detected, along with a bacterial community that was shared among the seagrasses. OTUs belonging to the shared seagrass community were mostly of the orders rhizobiales. Desulfobacterales was the most abundant order associated with the roots and Rhodobacterales with the leaves of the three seagrass species. Species-specific bacteria are represented mostly by OTUs of the same orders as the common OTUs, along with a few species-specific orders. The high abundant and widespread bacterial OTUs were identified to be mostly associated with sulfur and nitrogen cycling, which point towards the importance of these processes in seagrass fitness.