"We hope that this federal case will signal the end of this racist behavior and will help vindicate all of the victims who have suffered over the years," U.S. Attorney André Birotte Jr. said.
Sixteen of the people named in the indictment were arrested Tuesday, while another 23 were already in custody, U.S. attorney's spokesman Thom Mrozek said. Authorities were seeking another 12 suspects.
The crackdown is the latest effort by law enforcement to cripple Latino gangs that have targeted blacks in the Los Angeles area.
In 2009, more than 140 members and associates of the Varrio Hawaiian Gardens gang were charged in connection with waging a racist campaign against black people. Four years ago, authorities arrested dozens of members of South Los Angeles' Florencia 13 gang in connection with the killing of blacks because of the color of their skin.
Tuesday's charges mirrored a similar effort taken by federal prosecutors against The Avenues, a gang from the Highland Park area northeast of downtown Los Angeles, where four gang members were convicted in 2007 of hate crimes for killing a black man.
In Azusa, six people have been charged with civil rights violations for allegedly harassing, and in some cases attacking, African Americans to drive them out of the city or to prevent them from relocating there. Most of the defendants named in the indictment face a minimum 10-year prison sentence.
More than two-thirds of Azusa is Hispanic, while roughly 3 percent is black. The city has tried to address the racial problem after the number of hate crimes peaked at 17 in 2000 then dropped to about one a year since 2006, said Azusa Police Chief Robert Garcia.
City officials have also created a human relations commission in the wake of the gang's attempt to drive black residents from Azusa.
"Crimes based upon hatred are intolerable in our society and represent the worst in human behavior," Garcia said.
In one instance, prosecutors said Marty Michaels, known as "Casper," and another Varrio Azusa 13 member punched a black man in January 2000 while using a racial epithet. In April 2010, Manuel Jimenez yelled a racial slur at a black high school student returning home from a track meet, the indictment said. Jimenez and another man hit the student, chased him down the street and stole his items, prosecutors said.
Gang member Ralph "Swifty" Flores was sentenced to death in 2008 after he was convicted of four murders. A judge imposed three death sentences for three murders between 2002 and 2004 as well as a sentence of life without parole for the racially motivated murder of black teen Christopher Lynch in 1999. Flores was 17 at the time of the murder and not eligible for the death penalty because he was a minor.
Authorities also said the gang extorted payments from drug dealers to let them keep working in Azusa. The gang also drew up a business plan to monopolize the drug trade in the city, which included stockpiling an arsenal of weapons and plotting to kidnap relatives of wayward dealers, the indictment said.
Drug proceeds were then funneled to members of the Mexican Mafia who wielded control over the gang. The "13" in the gang's name -- much like others in Southern California -- stands for the letter `M' and shows the affiliation with the notorious prison gang.