Seagrass meadows are important coastal ecosystems that are declining worldwide. Given the profound impact of the microbiome on plant health, exploration of the seagrass microbiome is critical for proper ecosystem management and conservation. Although prior studies have investigated seagrass‐associated bacteria, fungi, and protists, virtually nothing is known about viruses infecting these flowering marine plants. Here, we report genomic and microscopic evidence of a new positive‐sense, single‐stranded ribonucleic acid virus infecting apparently healthy Thalassia testudinum in Florida. The virus, named turtlegrass virus X (TVX), shares 66% genome‐wide pairwise identity with foxtail mosaic virus, a potexvirus that infects terrestrial grasses. Quantitative polymerase chain reaction revealed TVX presence in 10% to 80% of T. testudinum leaves from two Tampa Bay sampling locations in February and August 2017, with an average viral load of 4.65 × 108 copies per mg leaf tissue. The discovery of TVX advances seagrass microbiome research, prompting further studies to assess its ecological impact.