From 1850 Bishop Viard sent priests occasionally to visit Otago and Southland. The first resident missionary, Father Delphine Moreau, S.M., sent by Viard in 1861 to found the Otago mission, laid in 1862 the foundation stone of St. Joseph's Church, a brick building still standing and serving as a school, near the site of the present St. Joseph's Cathedral. Bishop Viard blessed the church in October 1864.

In 1869 Otago and Southland were separated from the see of Wellington and erected into the diocese of Dunedin. The first Bishop, Patrick Moran, was at the time of his appointment Vicar Apostolic of the Eastern Province of Cape Colony, South Africa, and came to New Zealand in February 1871. Accompanying him were Father W. Coleman and 10 Dominican nuns who were to open the first of a series of schools in the new diocese. The Catholics in the diocese numbered about 6,000 at the time and under Moran's vigorous leadership built St. Joseph's Cathedral, 25 new churches, and 17 schools, besides several presbyteries and convents.