The Java War of 1825-30 constituted the last resistance of the Javanese aristocracy to Dutch rule. Its central figure was Pangeran Diponegoro (ca. 1785-1855), eldest son of the sultan of Yogyakarta. His education and disposition combined both Islamic and mystical elements: he was well acquainted with the teachings of the traditional Islamic schools (pesantren) in the rural village where he lived as a child with his grandmother, but he also experienced a vision in which the Goddess of the Southern Ocean promised that he was a future king. According to M.C. Ricklefs, Diponegoro was in a unique position to mobilize both the elite and the common people against the colonialists: "as a senior prince, he had access to the aristocracy, as a mystic to the religious community, and as a rural dweller to the masses in the countryside."

The immediate cause of Diponegoro's revolt in 1825 was the Dutch decision to build a road across a piece of his property that contained a sacred tomb. Thereupon ensued the Java War, a bitter guerrilla conflict in which as many as 200,000 Javanese died in fighting or from indirect causes (the population of Java at the end of the eighteenth century was only 3 million). Although the revolt was led by Diponegoro and other aristocrats, its considerable popular appeal, based on Islam and Javanese mysticism, created a scenario similar to twentieth-century wars in Southeast Asia. Insurgency was suppressed only after the Dutch adopted the "fortress system": the posting of small units of mobile troops in forts scattered through the contested territory. Diponegoro was arrested in 1830 and exiled for a short time to Manado in northern Sulawesi and then to Makassar where he died. The territories of Yogyakarta and Surakarta were substantially reduced, although the sultans were paid compensation.

The Java War was not a modern anticolonial movement. Diponegoro and his followers probably did not want to restore an idealized, precolonial past. Nor did they envision an independent, modern nation. Rather they sought a Javanese heartland free of Dutch rule. Because of his anti-Dutch role, Diponegoro is one of modern Indonesia's national heroes.

The Java War gave considerable impetus to a conservative trend in Dutch colonial policy. Rather than reforming their regime in the spirit of Daendels and Raffles, the Dutch continued the old VOC system of indirect rule. As it evolved during the nineteenth century, the Dutch regime consisted of a hierarchy in which the top levels were occupied by European civil servants and a native administration occupied the lower levels. The latter was drawn from the priyayi class, an aristocracy defined both by descent from ancient Javanese royal families and by the vocation of government service. The centerpiece of the system was the bupati, or regents. Java was divided into a number of residencies, each headed by a Dutch chief administrator; each of these was further subdivided into a number of regencies that were formally headed by a Javanese regent assisted by a Dutch official. The regency was subdivided into districts and subdistricts and included several hundred villages. The states of Surakarta and Yogyakarta remained outside this system. However, both they and the local regents lost any remnant of political independence they had enjoyed before the Java War. The sultanates played an important cultural role as preservers of Java's traditional courtly arts, but had little or no impact on politics.