The most feared, Aitarak or Thorn, noted for their black shirts, red berets and sunglasses, are headed by Eurico Guterres, who has said that if voters chose independence, East Timor would be turned into "a sea of fire".
Some of the militias can be traced to 1975 when Indonesia invaded East Timor and began arming groups to help bolster the union with Jakarta.
The Suharto regimeused the militias to help it to counter the threat from Falintil, the pro-independence guerrillas.
Other militias have surfaced since the change of regime in Jakarta and the preparations for the referendum.
The Indonesian military is believed to be arming the militias, which have killed at least 1,000 civilians in the past year.