Black was placed in Mexican federal custody on suspicion of "human trafficking" and "possession of wildlife species," state prosecutors said.
According to Mexican authorities, Black is also being investigated in connection with the killings of the three Americans -- a boy and two men -- whose bodies were discovered Sept. 10 in Rancho El Negro, or Black Ranch, about three miles from the site of last weekend's raids. Black has not been formally charged in the killings.
Mexican authorities identified the victims only as Michael B., 15; Robert W.B., 19; and Jesse L.B., 23.
Details about the killings are sparse, but Mexican news reports indicate that the three were gunned down execution-style at the entrance to a trailer home.
Some media accounts have suggested that the trio shared the surname Black. But their exact relation to the detained polygamist has been unclear.
On Wednesday, however, Felix Gonzalez, a spokesman for the Chihuahua prosecutor's office, confirmed that two of the victims -- Michael B. and Robert W.B. -- were Black's sons. The parentage of the third victim, Jesse L.B., had not yet been ascertained, Gonzalez said.
"The motive has not been clarified and is still being investigated," Gonzalez said of the killings.
The victims were found on one of five area properties owned by Black, the spokesman said.
The ranch where the slain men were found, like the settlement where Black was arrested, is situated in the sprawling Chihuahua municipality of Cuauhtemoc, hub of the region's large Mennonite population.
It was unclear why the accused pedophile chose to hide out and set up his own polygamist commune amid land settled by agrarian Mennonite communities. The two groups would appear to be unlikely neighbors. Mennonites, who began settling in Mexico in the 1920s after emigrating from Canada, practice a conservative, pacifist Christian faith that views marriage as a lifelong monogamous commitment between a man and a woman.