To a significant degree, the striking variations in the practice and interpretation of Islam — in a much less austere form than that practiced in the Middle East — in various parts of Indonesia reflect its complex history. Introduced piecemeal by various traders and wandering mystics from India, Islam first gained a foothold between the twelfth and fifteenth centuries in coastal regions of Sumatra, northern Java, and Kalimantan. Islam probably came to these regions in the form of mystical Sufi tradition. Sufism easily gained local acceptance and became synthesized with local customs. The introduction of Islam to the islands was not always peaceful, however. As Islamized port towns undermined the waning power of the east Javanese Hindu/Buddhist Majapahit kingdom in the sixteenth century, Javanese elites fled to Bali, where over 2.5 million people kept their own version of Hinduism alive. Unlike coastal Sumatra, where Islam was adopted by elites and masses alike, partly as a way to counter the economic and political power of the Hindu-Buddhist kingdoms, in the interior of Java the elites only gradually accepted Islam, and then only as a formal legal and religious context for Javanese spiritual culture.

These historical processes gave rise to enduring tensions between orthodox Muslims and more syncretistic, locally based religion — tensions that were still visible in the early 1990s. On Java, for instance, this tension was expressed in a contrast between the traditionalist santri and abangan, an indigenous blend of native and Hindu-Buddhist beliefs with Islamic practices sometimes also called Javanism, kejawen, agama Jawa, or kebatinan. The terms and precise nature of this opposition were still in dispute in the early 1990s, but on Java santri not only referred to a person who was consciously and exclusively Muslim, santri also described persons who had removed themselves from the secular world to concentrate on devotional activities in Islamic schools called pesantren--literally the place of the santri.

In contrast to the Mecca-oriented philosophy of most santri, there was the current of kebatinan, which is an amalgam of animism, Hindu-Buddhist, and Islamic — especially Sufi — beliefs. This loosely organized current of thought and practice, was legitimized in the 1945 constitution and, in 1973, when it was recognized as one of the agama, President Suharto counted himself as one of its adherents. Kebatinan is generally characterized as mystical, and some varieties were concerned with spiritual self-control. Although there were many varieties circulating in 1992, kebatinan often implies pantheistic worship because it encourages sacrifices and devotions to local and ancestral spirits. These spirits are believed to inhabit natural objects, human beings, artifacts, and grave sites of important wali (Muslim saints). Illness and other misfortunes are traced to such spirits, and if sacrifices or pilgrimages fail to placate angry deities, the advice of a dukun or healer is sought. Kebatinan, while it connotes a turning away from the militant universalism of orthodox Islam, moves toward a more internalized universalism. In this way, kebatinan moves toward eliminating the distinction between the universal and the local, the communal and the individual.

Another important tension dividing Indonesian Muslims was the conflict between traditionalism and modernism. The nature of these differences was complex, confusing, and a matter of considerable debate in the early 1990s, but traditionalists generally rejected the modernists' interest in absorbing educational and organizational principles from the West. Specifically, traditionalists were suspicious of modernists' support of the urban madrasah, a reformist school that included the teaching of secular topics. The modernists' goal of taking Islam out of the pesantren and carrying it to the people was opposed by the traditionalists because it threatened to undermine the authority of the kyai (religious leaders). Traditionalists also sought, unsuccessfully, to add a clause to the first tenet of the Pancasila state ideology requiring that, in effect, all Muslims adhere to the sharia. On the other hand, modernists accused traditionalists of escapist unrealism in the face of change; some even hinted that santri harbored greater loyalty towards the ummah (congregation of believers) of Islam than to the secular Indonesian state.

Despite these differences, the traditionalist Nahdlatul Ulama (literally, Revival of the Religious Scholars, also known as the Muslim Scholars' League), the progressive Consultative Council of Indonesian Muslims (Masyumi), and two other parties were forcibly streamlined into a single Islamic political party in 1973--the United Development Party (PPP). Such cleavages may have weakened Islam as an organized political entity, as demonstrated by the withdrawal of the Nahdlatul Ulama from active political competition, but as a popular religious force Islam showed signs of good health and a capacity to frame national debates.

The leading national "modernist" social organization, Muhammadiyah, has branches throughout the country and approximately 30 million followers. Founded in 1912, Muhammadiyah runs mosques, prayer houses, clinics, orphanages, poorhouses, schools, public libraries, and universities. On February 9, Muhammadiyah's central board and provincial chiefs agreed to endorse the presidential campaign of a former Muhammadiyah chairman. This marked the organization's first formal foray into partisan politics and generated controversy among members.

Nahdlatul Ulama (NU), the largest "traditionalist" social organization, focuses on many of the same activities as Muhammadiyah and indirectly operates a majority of the country's Islamic boarding schools. Claiming approximately 40 million followers, NU is the country's largest organization and perhaps the world's largest Islamic group. Founded in 1926, NU has a nationwide presence but remains strongest in rural Java. The Islam of many NU followers has heavy infusions of Javanese culture, and followers tend to reject a literal or dogmatic interpretation of Islamic doctrine. Many NU followers give great deference to the views, interpretations, and instructions of senior NU religious figures, alternately called "Kyais" or "Ulama." The organization has long advocated religious moderation and communal harmony.

The Indonesian Islamic Propagation Institute (LDII) has long been misunderstood by many Indonesians, with the enormous amount of black propaganda launched against them. Nevertheless, the number of the adherers of this organization continue to grow (Wakhid Sugiyarto, Kajian tentang Proses Santrinisasi ). LDII has a bi-monthly magazine named Nuansa Persada that includes a lot of news about activities and/or events that have been held by its adherers.

A number of smaller Islamic organizations cover a broad range of Islamic doctrinal orientations. At one end of the ideological spectrum lies the controversial Islam Liberal Network (JIL), which aims to promote a pluralistic and more liberal interpretation of Islamic thinking. Equally controversial are groups at the other end of this spectrum such as Hizbut Tahrir Indonesia (HTI), which advocates a pan-Islamic caliphate, the Indonesian Mujahedeen Council (MMI), which advocates implementation of Shari'a as a precursor to an Islamic state, and the sometimes violent Front Pembela Islam (FPI). Countless other small organizations fall between these poles.

Separate from the country's dominant Sunni Islam population, a small minority of persons subscribe to the Ahmadiyah interpretation of Islam. However, this group maintains 242 branches throughout the country. In 1980 the Indonesian Council of Ulamas (MUI) issued a "fatwa" (a legal opinion or decree issued by an Islamic religious leader) declaring that Ahmadiyah is not a legitimate form of Islam.

In addition there are small numbers of other messianic Islamic groups, including the Malaysian-affiliated Darul Arqam, and the syncretist Indonesian Jamaah Salamulla group (also called the Salamulla Congregation or The God's Kingdom). Its leader, Lia Eden, is currently facing charges of disdaining Islam and many Islamic organizations in Indonesia consider them as a heretic form of Islam.

History

Pre Europeans arrival

Islam was introduced in the Indonesian archipelago by means of sea trading. It first grew up in coastal cities throughout Malacca Strait, which is the gateway to the archipelago from the Middle East. It is uncertain of who brought Islam at the first place. Based on historical monuments, travel logs and old inscriptions, traders from Gujarat, India are the most likely to have introduced Islam in Indonesia.

The oldest historical account of the presence of Islam in the area is found in Leran, near Surabaya, the capital of East Java province. It is an epitaph of a non-native Muslim woman, estimated date between AD 1082–1102. A tombstone in Aceh written in Arabic language tells about Sultan Malik al Saleh who died in AD 1297. Al Saleh was a sultan of Samudera Pasai who was converted to Islam. Samudera Pasai is the first Muslim state in the archipelago, though it was only a small kingdom in a coastal area. Pasai name was derived from Parsi to indicate of Parsi-Indian immigrants from Gujarat who settled in the northern coast of Sumatra.

Due to its regional position in a sea trading route between China and Europe, Samudera Pasai was visited several times by notable explorers. Marco Polo in his itinerary mentioned about the presence of "Mooros" (notorious name of Muslim by Europeans in the medieval time) in Ferlec (Peureulak). Ibn Battutah, a Moroccan traveller, visited the kingdom in AD 1345–1346. In his travel log, Ibn Battutah wrote that the ruler of Samudera Pasai was a Mohammedan, who performs his religious duties in his utmost zeal. The madh'hab he used was Imam Shafi'i with the similar customs he had seen in India.

In the period between 1405–1433, the archipelago was visited by a Chinese emissary, Ma Huan, who was a Muslim. He was one of the envoys from the Chinese Emperor Yongle. In his report, he mentioned that the main states of the northern part of Sumatra were already Islamic. In 1414, he visited the King of Malacca, who was Muslim and also his people, and they were very strict believers. He also visited Java island and mentioned of "foreign Muslim colonies" in the East Java harbors. The native population, however, was still Hindus. He saw many Chinese immigrants; among them were Muslims.

The spreading of Islam throughout the archipelago had the same pattern. In Malacca, Javanese colony was founded in 1300. Newcomers from Java became Muslim. Upon their return to Java, they formed Muslim cells that spread to their families and relatives. When their ruler embraced Islam, the new Islamic state was born. Then Java traders came to the Molucca Islands. By the same pattern, a new sultanate in Ternate was formed in 1464.

In the late fifteenth century, the powerful Majapahit Empire in Java was at its decline. After had been defeated in several battles, the last Hindu kingdom in Java fell under the rising power of Islamized state Sultanate of Demak in 1520. Islam in Java then began to spread formally, largely influenced by the Wali Songo (or the Nine Saints).

European colonization

Post Independence

Islam is Indonesia's dominant religion with approximately 88% of its population identifying as Muslims, making it the most populous Muslim-majority nation in the world.

The Indonesian Central Statistic Bureau (BPS) conducts a census every 10 years. The latest data available, from 2000, drew on 201,241,999 survey responses; the BPS estimated that the census missed 4.6 million persons. The BPS report indicated that 88.22 percent (210 million in 2004) of the population label themselves Muslim, 5.87 percent Protestant, 3.05 percent Catholic, 1.81 percent Hindu, 0.84 percent Buddhist, and 0.2 percent "other," including traditional indigenous religions, other Christian groups, and Judaism. The country's religious composition remains a politically charged issue, and some Christians, Hindus, and members of other minority faiths argue that the census undercounted non-Muslims.

Most Muslims are Sunni, although some follow other branches of Islam, including the Shia, who number approximately 100,000 nationwide. In general the mainstream Muslim community belongs to two orientations: "modernists," who closely adhere to scriptural orthodox theology while embracing modern learning and modern concepts; and predominantly Javanese "traditionalists," who are often followers of charismatic religious scholars and organized around Islamic boarding schools.