A new epibiontic ciliate of the genus Metacystis is described on the seagrass Thalassia testudinum of the coral reef lagoons of Veracruz, Mexico. The ciliate was studied in living and stained specimens and under the scanning electron microscope. The cell body (10–35 × 10–18 μm in vivo) is transversely annulated (4–6 rings). The somatic ciliature consists of 22–30 longitudinal kineties, and patterned as 5–7 transverse kineties. The circumoral kinety is composed of kinetosomes closely spaced. The macronucleus diameter measures about 3–7 μm. The lorica (18–61 × 11–26 μm) has the posterior end round to conical or irregular with mucoid filaments. This prostomatid colonizes both natural and artificial substrates placed in an aquarium. Metacystis borrori n. sp. is a species that forms part of the ciliate community on Thalassia testudinum with a temperature range of 21–26 °C and a salinity of 32–40‰.