RSF urged South Sudan's authorities "to shed all possible light" on the murder of freelance reporter Isaac Vuni, who was kidnapped on June 4 along with his brother from the family's home in southern Kerepi, near the Ugandan border.
Responsibility for the abduction was never claimed.
Vuni's relatives told the independent Sudan Tribune newspaper that his body was discovered on a farm outside Kerepi, RSF said in a statement. His brother has yet to be found.
"We condemn Isaac Vuni's foul murder and call on the authorities to conduct an investigation to identify those responsible and bring them to justice," said Clea Kahn Sriber, the head of RSF's Africa desk.
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Vuni, who often wrote for the Sudan Tribune, had been arrested in Juba in 2009 after reporting that members of the Sudan People's Liberation Army and the South Sudanese government were implicated in a financial scandal.
Seven journalists were killed in South Sudan last year, according to another media rights group, the Committee to Protect Journalists.
RSF said journalists have been regularly targeted since the civil war began in 2013, with many held incommunicado, including Radio Miraya's George Livio -- now held incommunicado for more than two years.
South Sudan was this year ranked 140th out of 180 countries in RSF's global press freedom index, 15 places lower than the previous year.