Indigenous people are almost invisible in El Salvador. This comes from a history of repression throughout the 20th century. From a World Bank report:
Salvadoran Indigenous People are descendants of the Pupils, a nomadic tribe of the Nahua of Central Mexico, the Mesoamerican Lenca and the South-American Chibcha. From the beginning of the Spanish conquest in El Salvador, the Indigenous and the Spaniards lived in the same areas. Racial mixing known as mestizaje began in the XVI century. With the development of the indigo plantations in the early XVII century, many indigenous villages were destroyed, and many were forced to farm and work on these plantations. In the infamous la matanza, masacre of 1932, 50,000 indigenous were killed in retaliation of an indigenous upheavel to protest government policies. After this event, the indigenous began to hide their traditions and to assimilate to the dominant ladino society quietly.
The World Bank performed a "social assessment" in El Salvador in 2005 and estimated the indigenous population to be between 150,000 to 200,000 people. Indigenous peoples are likely to live in rural areas and be subject to the conditions of poverty afflicting the rural poor in the country.
There are starting to be some efforts to preserve what is left of indigenous culture. IndianCountry.com has a story about one effort in Morazan department in rural northeastern El Salvador to maintain the traditions of the Kakawira, a Mayan indigenous people. The World Bank's loan which supports "Red Solidaria," the Saca administration anti-poverty program, has an indigenous peoples protection program as part of its requirements.