In the Eastern Christian Churches (Orthodox, Oriental Orthodox and Eastern Catholic), the term exarch has two distinct uses: the deputy of a patriarch, or a bishop who holds authority over other bishops without being a patriarch (thus, a position between that of patriarch and metropolitan); or, a bishop appointed over a group of the faithful not yet large enough or organized enough to be constituted an eparchy/diocese (thus the equivalent of a vicar apostolic).
After the fall of the Western Empire in 476, the Eastern Roman Empire remained stable through the beginning of the Middle Ages and retained the ability for future expansion. Justinian I reconquered North Africa, Italy, Dalmatia and finally parts of Spain for the Eastern Roman Empire. However, this put an incredible strain on the Empire's limited resources. Subsequent emperors would not surrender the re-conquered land to remedy the situation. Thus the stage was set for Emperor Maurice to establish the Exarchates to deal with the constantly evolving situation of the provinces.
In Italy the Lombards were the main opposition to Byzantine power. In North Africa the Amazigh or Berber princes were ascendant due to Roman weakness outside the coastal cities. The problems associated with many enemies on various fronts (the Visigoths in Spain, the Slavs and Avars in the Balkans, the Sassanid Persians in the Middle East, and the Amazigh in North Africa) forced the imperial government to decentralize and devolve power to the former provinces.
The term Exarch most commonly refers to the Exarch of Italy, who governed the area of Italy and Dalmatia, still remaining under Byzantine control after the Lombard invasion of 568. The exarchate's seat was at Ravenna, whence it is known as the "Exarchate of Ravenna". Ravenna remained the seat of the Exarch until the revolt of 727 over Iconoclasm. Thereafter, the growing menace of the Lombards and the split between eastern and western Christendom that Iconoclasm caused made the position of the Exarch more and more untenable. The last Exarch was killed by the Lombards in 751.
A second exarchate was created by Maurice to administer northern Africa, formerly a separate praetorian prefecture, the islands of the western Mediterranean and the Byzantine possessions in Spain. The capital of the Exarchate of Africa was Carthage. The exarchate proved both financially and militarily strong, and survived until the Arab Muslim conquest of Carthage in 698.
The principle became that, since no addition should be made to the fixed number of five patriarchs of the pentarchy, any bishop with authority over other bishops who was not dependent on any one of these five should be called an exarch. Thus, since the Church of Cyprus was declared autocephalous (at Ephesus in 431), its Primate received the title of Exarch of Cyprus.
The short-lived medieval Churches of Ipek (for Serbia), Achrida (for Bulgaria) and Tirnova (for Romania), were governed by exarchs, though these prelates occasionally assumed the title of patriarch (Fortescue, Orthodox Eastern Church, 305 sq. 317 sq., 328 sq.). On the same principle the Archbishop of Mount Sinai is an exarch, though in this case, as in that of Cyprus, modern Orthodox usage generally prefers the title "Archbishop".
After imperial Russia destroyed in 1802 the old independent Georgian Church (autocephalous since 750, and whose head was since 1008 styled Catholicos-Patriarchs of Iberia, i.e. the Caucacus), the Primate of Georgia (always a Russian) sat in the Holy Synod at St. Petersburg with the title of Exarch of Georgia (Fortescue, Orthodox Eastern Church, 304-305). On 7 April 1917 the Georgian Patriarchate was restored for the Archbishops of Mtsheta and Tbilisi, with the style Catholicos-Patriarch of All Georgia; in 1943 its autocephaly was recognized by Russia, and on 3 March 1990 the Georgian Patriarchate was recognized by Constantinople.
After the dismembering of the Ottoman Empire, which like the Byzantine empire had ruled most of Orthodoxy (allowing quite some autonomy under the millet system - see Ethnarch), the pentarchy-number principle, already abandoned in the case of Russia, gave way to the desire of the now politically independent orthodox nations to see their sovereignty reflected in ecclsiastical autonomy - autocephaly - and the symbolic title to crown it: a 'national' Patriarch. There are now about twenty Patriarchs.
In the Eastern Orthodox Church, an Exarch is now a deputy of a Patriarch. In many cases he rules on behalf of the Patriarch a Church outside the home territory of the Patriarchate. Thus, in the United States of America, there are Exarchs representing, among others, the Serbian, Romanian, Bulgarian and Jerusalem Patriarchs. The style of the Exarchs of the Patriarchate of Jerusalem is "Exarch of the Holy Sepulcher".
The Mexican Orthodox parishes in five deaneries (Mexico City, D.F., State of Mexico, State of Jalisco, State of Veracruz and State of Chipas) of the Orthodox Church in America are governed as the "Exarchate of Mexico," with Archbishop Dmitri of Dallas and the South serving as Exarch of Mexico concurrently with his responsibilities for the southern United States. 
The Oriental Orthodox Patriarch of Antioch currently has under his authority an Exarch in India, known by the ancient title Maphrian, although he is popularly referred to as Catholicos. This is not to be confused with the autocephalous Catholicate of the East, which is also located in India.
In Eastern Catholic Churches (of Eastern tradition but in full communion with the Bishop of Rome, the Pope), the ecclesiastical title of Exarch is in common use.
These Churches are, in general, not identified with a particular liturgical rite. Thus, no less than fourteen of them use the one same Byzantine Rite, mostly in one or other of only two languages, Greek and Church Slavonic, but they maintain their distinct identities. The use of the word "Rite" (with upper-case R) to refer to these Churches has largely, though not altogether, fallen into disuse and can lead to confusion with the liturgical sense of the word "rite" (see Eastern Catholic Churches). Because of population shifts, half or so of these Churches have not just exarchates but full-scale eparchies or even archeparchies outside their original territory.
An Apostolic Exarch is a Bishop of a titular see to whom the Pope, as Bishop of the Roman See of the Apostle Peter, has entrusted the pastoral care of the faithful of an autonomous particular Church in an area, not raised to the rank of eparchy, that is situated outside the home territory of an Eastern Church. An Apostolic Exarch thus corresponds to what in the Latin Rite is called a Vicar Apostolic. These exarchates are generally immediately subject to the Holy See, with limited over site by the patriarch, major archbishop, or metropolitan of the Eastern Church.
Patriarchs and Major Archbishops may also appoint Exarchs (not always bishops). These Patriarchal or Archiepiscopal Exarchs are limited to the traditional territory of their church. They may be suffragan to an archdiocese or archeparchy of the Eastern Church, or be immediately subject to the patriarch or major archbishop.
The 2006 Annuario Pontificio listed the following Catholic Exarchates.