It was the first known case of an entire Israeli Arab family joining up with the jihadist organisation, said a spokeswoman for the Shin Bet domestic security agency.
Wissam, 41, and Sabreen Zbedat, 30, from the northern Israeli town of Sakhnin, flew to Romania in June 2015 with their children aged three, six and eight, the Shin Bet and Israeli police said in statements.
From there they travelled to Turkey, Syria and on to Iraq, where IS recruited them, the authorities said.
Wounded in the leg, he was hospitalised in the IS stronghold of Mosul where his family was staying.
Sabreen worked at a hospital in the northern city and the children attended schools, the police said.
They decided to leave Mosul because of international coalition bombardment, harsh conditions imposed by IS and pressure from relatives in Israel.
The return journey took eight months, according to the Israeli police.
After several failed attempts they passed from Syria into Turkey, paying thousands of dollars to smugglers, but were arrested by the Turks after crossing the border.
The parents were charged today in Haifa district court on counts of joining a terror organisation and visiting an enemy country.
Several Arabs from northern Israel have been arrested for alleged links with IS and around 50 Israeli Arabs are believed to be among its ranks in Syria and Iraq at present.
Israeli Arabs are the descendants of Palestinians who remained on their land after the creation of Israel in 1948.
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