The earliest part of St John’s is believed to be the tower, which dates from about 1400. The remainder was rebuilt around 1450, including the construction of the north and south arcades. In c. 1520 the south aisle was extended eastward to form a chapel for the Gilbert family of Compton Castle.  In 1874 the chancel was restored and many of the windows were replaced.

There is a good deal of graffiti surviving in the church. Most of it is found around the doorways, especially the south door, on a number of the limestone piers, and on an effigy located in the chancel.

On the porch doorway are the letters AM. These may be initials, but these letters are also recognised as a Marian reference (Virgin Mary) – and possibly meaning Ave Maria. The compass drawn circles and notches/ladder on the south doorway are likely to have been seen as apotropaic (protective), as are the asterisk type symbols and saltire cross found within the church itself.

There are, unusually, images of birds, several of which survive only in part, having probably been eroded by cleaning/scraping during refurbishments. The birds are on a pier in the south aisle, close to the church door, with another (feet and part of body detectable) by the doorway of the room over the porch. From what can be seen, they all seem to be the same design. Their purpose and meaning are not known.

Marldon, St John the Baptist