Rockwell worked with Black separatist leaders who shared his goal of racial segregation, such as Elijah Muhammad and Malcolm X. In January 1962, Rockwell wrote to his followers that Elijah Muhammad has gathered millions of the dirty, immoral, drunken, filthy-mouthed, lazy and repulsive people sneeringly called 'niggers' and inspired them to the point where they are clean, sober, honest, hard working, dignified, dedicated and admirable human beings in spite of their color ... Muhammad knows that mixing is a Jewish fraud and leads only to aggravation of the problems that it is supposed to solve ... I have talked to the Muslim leaders and am certain that a workable plan for separation of the races could be effected to the satisfaction of all concerned—except the Communist-Jew agitators.

He also said of Elijah Muhammad "I am fully in concert with their program, and I have the highest respect for Elijah Muhammad." He referred to Muhammad as "The Black People's Hitler" and donated $20 (worth about $204 in 2022) to the Nation of Islam at their "Freedom Rally" event on June 25, 1961, at Uline Arena in Washington where he and ten ANP members attended a speech by Malcolm X. Rockwell gave a speech to a crowd of 12,000 at a Black Muslim event in the International Amphitheater in Chicago, with Elijah Muhammad and Malcolm X, on February 25, 1962

Inspired by Black Muslims' use of religion to mobilize people, Rockwell sought to collaborate with Christian Identity groups. On June 10, 1964, he met and formed an alliance with Identity minister Wesley A. Swift. Rockwell used religious imagery, depicting himself as a Christ-like martyr who was fighting against the Jews. Nazis found a welcome home in Swift's church and church members found a political outlet in the American Nazi Party.