Before the reformation, nearly the whole of the county was part of the Diocese of Ardfert and Aghadoe, with the cathedral at Ardfert. The parish of Kilcaskan was part of the Diocese of Cloyne, while the townland of Killmurrily was in the Diocese of Limerick.
Following the reformation, the (Anglican) Protestant Church of Ireland came into possession of the ancient churches, but as only about 2% of the county's population were protestant, most them fell into disuse and ruin. Ardfert Cathedral was destroyed in 1641, and the Diocese was combined with Limerick from 1663. A number of new churches were built at the beginning of 19th Century. When the Church of Ireland was disestablished in 1871, all the unused places of worship and burial grounds were handed over to the local authorities. A further decline in the Protestant population followed the creation of the Irish Free State, and a number of churches have been deconsecrated or demolished, and parishes combined. The diocese now contains 15 churches.
The majority of the population belonged to the Roman Catholic church. The last Catholic Bishop of Ardfert was ejected from the Cathedral by English forces in 1579. The church had to become an underground one, and the parish system became confused. Eventually, the episcopate was permanently restored to the renamed Diocese of Kerry. The parish structure was established by combining old parishes, new churches built, and the Cathedral and Chapter reestablished at Killarney. Details of the present parishes can be found at the website of the Roman Catholic Diocese of Kerry.
The Catholic Encyclopedia on the Diocese of Kerry and Aghadoe