The Patriarchate is one of the smallest of the Oriental Orthodox Churches but one that has exerted a very significant political role and today still exercises a spiritual authority.

But Sultan Mehmed II asked the Armenians to establish their own church in the new Ottoman capital, as part of the Millet system.

Hovakim I was recognized as the religious and secular leader of all Armenians in the Ottoman Empire, and carried the title of milletbaşı or ethnarch as well as patriarch.

In 1896 Patriarch Madteos III (Izmirlian) was deposed and exiled to Jerusalem by Sultan Abdülhamid II for boldly denouncing the 1896 massacre[clarification needed].

The Armenian Patriarch of Constantinople Madteos III (Izmirlian) was permitted to return to Istanbul in 1908 when Sultan Abdulhamid II was deposed by the Young Turks.

However, in 1915 the Armenians suffered great hardship under the Young Turk administration owing to the desire of the Turkish government for its peoples to be religiously homogeneous (i.e., Muslim), motivated perhaps by an imagined threat of Armenians from Russian influences with whom Turkey was at war.

The inability of Turkey to acknowledge these events has been a source of significant angst among Armenians worldwide for the past hundred years.

Despite a huge diminution in the number of its faithful during the Armenian genocide, the patriarchate remains the spiritual head of the largest Christian community presently living in Turkey.

Some members of the Armenian community of Turkey criticised this move and asked for the election of a new Patriarch by universal suffrage instead.