St Mary's Church, Pentraeth is a small medieval parish church in the village of Pentraeth, in Anglesey, north Wales. The date of construction is unknown, but is probably from some time between the 12th to 14th centuries. A church dedicated to St Mary was recorded here in 1254, but there is a tradition that there was an older church dedicated to St Geraint, an early British saint. Some medieval stonework remains in three walls of the building (the west wall, and parts of the north and south walls). A chapel was added to the south side in the 16th or 17th century. The church was altered and refurbished during the 19th century, including an extensive rebuilding by Henry Kennedy, the architect for the Diocese of Bangor, in 1882. St Mary's is still used for worship by the Church in Wales, and is one of three churches in a combined parish.

St Mary's contains a number of memorials from the 18th and 19th centuries. Members of the families associated with Plas Gwyn, a nearby manor house, have their memorials in the chapel. John Jones, who was Dean of Bangor Cathedral from 1689 to 1727, was born at Plas Gwyn, and is commemorated with a stone tablet on the south wall of the chancel. Another native of Pentraeth, the cleric and writer Thomas Owen, who died in 1812, also has a tablet in the chancel. Charles Vivian, 2nd Baron Vivian (who died in 1886), and his wife Mary are remembered with a bronze tablet on the east wall of the chapel. There are other memorials on the walls of the chapel and the nave. The south window of the chapel has stained glass in memory of Claud Panton Vivian, of Plas Gwyn, who died at the age of 24 during the Second World War. The churchyard has a number of graves for members of the Vivian family, and their plot contains four beautifully-carved Celtic crosses. The churchyard also contains two Commonwealth war graves, of a South Lancashire Regiment soldier of World War I and a Royal Navy sailor of World War II.