The suspects, aged 51 and 53, face charges of sexual abuse of children and human trafficking for the purpose of sexual exploitation, according to the indictment read out in a Berlin district court.
The abuse allegedly occurred between 2002 and 2009 and involved 13 victims.
The youngest was aged six, while the others were between the ages of 10 and 13.
Prosecutors describe the suspects as being central to a paedophile network in the German capital that deliberately sought out boys from difficult backgrounds.
"The accused allegedly took advantage of this by offering to pay the boys for sexual services," court spokeswoman Lisa Jani told reporters.
The 51-year-old suspect stands accused of 379 instances of child abuse and acting as intermediary between the boys and other men, she added. His co-defendant faces 47 counts of abuse against minors.
A verdict is expected in April at the earliest.
Two other suspects aged 78 and 80 also face charges in connection with the case but the court has yet to determine if they are fit to stand trial.