The researchers from Gabon and the United States examined over 1,100 bats from ten species, but detected the virus' RNA genome and antibodies only in Rousettus aegyptiacus, a common fruit bat found all across sub-Saharan Africa.
Marburg and its deadly cousin Ebola virus have caused large outbreaks with extremely high fatality rates -- 80 to 90 percent -- in humans and great apes.
No vaccine or drug therapy has proven effective in warding off or curing the disease, which causes horrendous symptoms including internal bleeding, high fevers, coma and renal failure.
Death from shock usually occurs a week after clinical onset of symptoms.
The world's biggest outbreak of Marburg occurred in Angola from October 2004 to July 2005, infecting 374 people, 329 of whom died, according to an official toll.
The study reports finding viral RNA in four of 283 R. aegyptiacus bats collected in Gabon and the Republic of Congo in 2005 and 2006. Another 29 bats of the same species tested serologically positive for Marburg, showing traces of antibodies providing immunity against the virus.
Neither Marburg-virus RNA nor specific antibodies were detected in any of the other species of bats tested, according to the study, published in the online science journal PLoS ONE.
"Identifying Marburg infection in the African fruit bats brings us one step closer to understanding this deadly disease," said one of the study's authors, Eric Leroy of the Centre International de Recherches Medicales de Franceville in Gabon.
Scientists had been trying to pinpoint the "natural reservoir" of the virus ever since the initial outbreak among laboratory workers in Germany 40 years ago.
Bats became likely culprits after the recent discovery of the related Ebola virus in fruit bats in Gabon and the Republic of Congo, and an outbreak of Marburg hemorrhagic fever in a gold mine in the Democratic Republic of Congo containing a large number of the nocturnal flying mammals.
The fruit bats that tested positive for the disease are the first naturally-infected non-primates ever identified, the paper said.
It is also the first report of Marburg in this area of Africa, suggesting that the risk of further outbreaks may be higher than previously thought.
"From a public health perspective, this discovery offers us new insight into the transmission of Marburg virus and potentially other filoviruses," said lead author Jonathan Towner, a senior microbiologist at the Centers for Disease Control and Prevention in Atlanta, referring to the family of viruses that includes Ebola.
Marburg infections were recently reported among miners in Uganda, where another team of researchers captured bats for testing, the World Health Organization said last week.