Saint Mark’s is home to the largest and most comprehensive pipe organ in an Anglican parish church in the Greater Auckland region.

The first instrument in the original church building was actually a harmonium, which was replaced by a pipe organ in 1865. This organ was found in Wellington and is believed to have originally come from Hobart in the early convict days.

A new two manual and pedal organ of 19 speaking stops was installed in 1882. In order to house it properly, the church tower was built, with a new organ chamber in its base.

In 1920, this organ was enlarged and modified to a specification drawn up by the organist of St Mark’s, J. Maughan Barnett, who was also the City Organist. The instrument was very comprehensive and included a new choir division.

Following a fire in the Tower in 1935, the organ was extensively reconstructed at a cost of 2000 pounds. The new instrument was a lavish example of Edwardian organ building, retaining several ranks from the previous organ and incorporating the latest technology in exhaust-pneumatic action and console design.

Another substantial rebuild took place in 1977 in the prevailing neo-classical style of the time, complete with new console, and in 1989 the organ was partially reconstructed to return the chancel casework and façade to its original position.

Since 2001, the Saint Mark’s organ has undergone considerable tonal and mechanical refurbishment in order to improve acoustics within the church and enhance the organ’s role in congregational and choral accompanying. A full restoration of its winding system took place in 2009, and it was returned and rededicated on Advent Sunday of that year.