Ostoja Stanisic, 60, and Marko Milosevic, 48, were detained near the eastern town of Zvornik on orders of the Bosnian war crimes prosecutor, the prosecutor's office said in a statement.
The men are suspected of committing crimes in the area near the Petkovci dam in the village of Djurici, where around 1,000 Bosnian Muslim men and boys from Srebrenica were executed in July 1995, the office said.
Bosnian police said they had seized a large cache of weapons and ammunition during raids at several locations near Zvornik after the arrests.
The Srebrenica massacre involved the systematic slaughter of 8,000 Muslim men and boys after Bosnian Serb forces, commanded by General Ratko Mladic, captured the U.N.-protected Srebrenica enclave in July 1995.
The Petkovci dam was among several sites where Bosnian Muslim men from Srebrenica were executed.
Last week, the Bosnian war crimes court sentenced four former Bosnian Serb soldiers to the longest jail terms yet for their role in the mass execution of hundreds of Muslims at the Branjevo farm, another Srebrenica massacre site.
Bosnian Serb wartime leader Radovan Karadzic and Mladic are indicted of genocide in Srebrenica and their trials are under way at the U.N. International Criminal Tribunal for the former Yugoslavia in The Hague.
Darul Ihsan Media Desk