French nationals Cécile Kohler and Jacques Paris have been charged with "spying" for Israel, a Western diplomatic source and family sources told AFP.
Iranian officials have also charged the pair with "conspiracy to overthrow the regime" and "corruption on earth", the diplomatic source and Kohler's sister told AFP.
"All we know is that they have seen a judge who confirmed the three charges," said Kohler's sister.
News of the charges comes a day after a French diplomat was able to visit the two French nationals, whose families had demanded proof that they were alive after Israeli strikes.
The French foreign ministry did not specify where the visit occurred, amid uncertainty over the couple's whereabouts.
The fate of Kohler and Paris had been unknown since Israel targeted Tehran's Evin prison in an air strike last week, before a US-proposed ceasefire between the Middle East foes came into force.
Read moreImages and eyewitness accounts from Tehran's Evin Prison after an Israeli strike
Iran's judiciary said the Israeli strike on the prison had killed at least 79 people.
It has also said the Iranian prison authority transferred inmates out of Evin prison, without specifying their number or identifying them.
Several women prisoners have been transferred to Qarchak prison for women outside Tehran, which has a notorious reputation for its conditions.
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Kohler, 40, and Paris, her 72-year-old partner, have been held in Iran since May 2022 on espionage charges their families reject.
Iran is believed to hold around 20 European nationals, many of whose cases have never been publicised, in what some Western governments including France describe as a strategy of hostage-taking aimed at extracting concessions from the West.
Three Europeans, who have not been identified, have also been arrested in the wake of the current conflict, two of whom are accused of spying for Israel, according to the authorities.
(FRANCE 24 with AFP)