Habyarimana Mucebo, a senior member of the Rwandan FDLR rebel group, was captured in Rutshuru, north-eastern DR Congo.
Members of the FDLR fled into DR Congo after the 1994 genocide in Rwanda.
The slaughter of some 800,000 ethnic Tutsis and moderate Hutus sparked years of unrest in the region.
Mr Mucebo, the FDLR intelligence chief, has been taken into custody for interrogation, the army says.
Most senior figures of the group are wanted by Rwanda for their alleged role in the 1994 killings.
Mr Mucebo's arrest is not linked to genocide charges as initially reported.
Congolese officials accuse him of links to atrocities blamed on the FDLR.
For many years, the Hutu rebel group had become a source of instability in DR Congo's North Kivu province.
Rwanda has sent troops and militias into DR Congo on several occasions since the genocide, saying they were going after the FDLR.

The pro-Rouhani reformist group Omid (Hope) won all 21 seats, ousting their conservative rivals who had been in power for 14 years.
Mr Rouhani won Friday's presidential election in the first round.
He promised voters a moderate and outward-looking Iran and criticised the conservative-dominated judiciary.
Council elections were held alongside the presidential vote and the results were announced on Sunday.
The new city council must convene within 45 days when it will elect a new mayor to oversee services for Tehran's nine million residents.
Incumbent Mayor Mohammad Baqer Qalibaf was a candidate in the early stages of the presidential election but dropped out to back hardliner Ebrahim Raisi.
Mr Raisi only received 38.5% of the vote, which was not enough to take the election to a second round.
President Rouhani, 68, said his resounding victory showed that voters rejected extremism and wanted more links with the outside world.
Analysts say he is in a strong position to seek reforms and to revive Iran's ailing economy.
After his re-election there were celebrations in the capital, Tehran, with crowds of young people singing and dancing in the central Vali Asr Square.
In his first speech after the result was announced Mr Rouhani said: "The Iranian nation has chosen the path of interaction with the world, a path which is distant from extremism and violence."
Mr Rouhani supports the landmark deal with world powers to curb Iran's nuclear programme.

Leader Leanne Wood said her party accepted the referendum result to leave the European Union, but claimed no part of the UK voted for a "hard" Brexit.
In an article for The Times, she said the Welsh Government should not "sit back and let Brexit take its course".
Meanwhile First Minister Carwyn Jones has told AMs that UK ministers will have to compromise on immigration.
Ms Wood said the UK was "still in the dark" four months after the June vote on what the result meant.
She said Plaid accepted the High Court ruling that Parliament must give its approval for the triggering of Article 50, to formally launch the two-year process of the UK's departure from the EU.
Ms Wood said the ruling "should not be seen as an opportunity to overturn the result", but gave an opportunity for the 48% of voters who backed Remain "to have an input" and pursue a "soft" Brexit.
She accused the UK government of making "nothing but contradictory statements, with comments from one minister ridiculed by another", and claimed the Welsh Government had been "at best incoherent and at worst utterly clueless" in its response to Brexit.
"Wales voted Leave, but it does not mean that the Welsh government should sit back and let Brexit take its course," Ms Wood wrote.
"Our exit from the EU will be one of the most pivotal moments in our history and it is vital that both governments get it right."
Stressing her party's preference for continued membership of the single market, Ms Wood said Plaid AMs and MPs would table written questions on Brexit every day until ministers in both Westminster and Cardiff Bay gave a "satisfactory outline" of their intentions.
"People need and deserve answers, and Parliament needs answers before it can be expected to support the triggering of Article 50," she said.
A Rwandan Hutu rebel commander wanted for atrocities committed on Congolese soil has been arrested in eastern Democratic Republic of Congo.
[NEXT_CONCEPT]
Iran's re-elected moderate President Hassan Rouhani has received a further boost after reformists won key council elections in the capital, Tehran.
[NEXT_CONCEPT]
People need clarity on what Brexit means for both the UK and Welsh governments, Plaid Cymru has said.