"We've reached an agreement in principle with Robert Saleh to become our head coach," the Jets said in a statement.
Saleh has spent the past four years in Santa Clara, California, transforming the 49ers' defense from a onetime laughingstock to one of football's most elite units.
He'll take over a team that won just two of 16 games this past season and hasn't made the playoffs since the 2010-11 campaign. The Jets have just one Super Bowl title in franchise history, the famed Joe Namath guarantee of Jan. 12, 1969.
Before Saleh, 41, a native of Dearborn, Michigan, was hired by the Jets, no Muslim had ever been an NFL head coach, according to the Council on American-Islamic Relations, or CAIR, a Muslim civil rights advocacy group.
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"We welcome this development as another sign of the increasing inclusion and recognition of American Muslims in our diverse society," CAIR spokesman Ibrahim Hooper said in a statement late Thursday.
Saleh, whose family traces its roots to Lebanon, will be the fourth NFL head coach of Lebanese descent, according to two Arab American advocacy groups.
The new Jets head coach follows in the footsteps of Abe Gibran and Rich Kotite, according to the American-Arab Anti-Discrimination Committee.
Ed Khayat, the brother of former University of Mississippi Chancellor Robert Khayat, is also of Lebanese descent, the Arab American Institute said.
Gibran was head coach of the Chicago Bears for three seasons, 1972 to 1974, while Kotite ran the Philadelphia Eagles for four campaigns (1991-94) and the Jets for two years (1995-96). Khayat ran the sidelines in Philadelphia for two seasons (1971-72).
"Anytime you have a proud Arab American reach the pinnacle of their professional career it is an empowering moment for the entire community," Arab American Institute Executive Director Maya Berry said in a statement.
"The overwhelmingly positive public response to him achieving this level of success is clearly an indication of how much both Arab Americans and American Muslims are part of this moment. And, as another kid from Dearborn, Michigan, I am incredibly proud of one of our hometown heroes."
Saleh brings considerable credentials to his new job in East Rutherford, New Jersey. Before he took over the 49ers' defense in 2017, San Francisco had ranked dead last in total yards surrendered.
This season's accomplishments were particularly impressive in light of the staggering number of injuries that prevented many of Saleh's best players from taking the field.