The church of the Megali (Great) Panagia in the central square of Neapolis dominates all parts of the city, being the largest church of Eastern Crete. It is dedicated to the Dormition of Theotokos and during its celebration, on August 15, pilgrims from all over Crete arrive here. It is cruciform with a dome and two imposing belfries on the west. The marble surfaces, the wood-carved iconostasis (templon) and the modern frescoes of 1962-1965 impress the visitor. The exterior hosts tombs of local bishops.
The temple was built on the site of the monastery of Megali Panagia, which was named after a copy of the icon of the Megali Panagia (Holy Virgin Mary) from Jerusalem. The monastery of Megali Panagia was founded before the conquest of Eastern Crete by the Ottomans in 1645 and owned the entire town of Kenourgio Horio, that is, the current Neapolis. It was directly ruled by the Ecumenical Patriarch in Constantinople until 1713, when it was moved to the Diocese of Petra.
When all the monastery buildings and the cathedral were destroyed in the 19th century, residents asked the Turkish authorities to rebuild them. The bishop of Petra, Ioakeim Klontzas, received permission to rebuild the temple of the Virgin Mary, so in 1819 the small signle-nave church of the Great Panagia Fermalina, which we see today next to the large church, was built on the ruins of the old church. The name of Little Panagia was mistakenly used, as opposed to the modern larger metropolitan church, since the name Great Panagia pre-existed.
In 1883 the church of Panagia Fermalina was considered ready-to-collapse and the bishop asked a new permission to build the new church of Neapolis. Its construction took many years, as it was founded in 1889 by the Bishop Meletios Chlapoutakis, built mainly during the term of Bishop Titus Zografidis and was completed in 1927 by the Bishop Dionysios Maragoudakis. The temple was heavily damaged during World War II bombings and was repaired in 1963, when all traces of the old monastery were demolished.