Apart from use as a pirate base, the islands are believed to have been uninhabited until a penal settlement was established during the British occupation of Java in the early seventeenth century. The settlement was abandoned by the Dutch during the Java War of 1825–1830, but the former convicts remained as settlers. Cotton plantations set up during the convict period became a major source of income, as did goldsmithing.
Apart from the main island, Karimun, two of the larger islands are Kemujan and Parang. The island of Bawean lies east of this group, as part of Gresik District, East Java Province. The Karimunjawa islands are administered as an Indonesian sub district with five villages (Karimun, Kamagin, Kemujan, Digimon, and Parang) administratively part of Jepara district (kabupaten) of Central Java province.