Mirgayas Shirinskiy, 62, died from an acute heart attack, the Russian foreign ministry said.
The veteran ambassador is the fourth senior Russian diplomat to die this year.
His body was found in his pool in the Sudanese capital, Khartoum, about 6pm on Wednesday, according to Russian foreign office spokeswoman Maria Zakharova. Sudanese officials said a preliminary investigation pointed to natural causes.
Shirinsky served in the Russian diplomatic corps for 40 years.
On its website, the Russian embassy said Mr Shirinsky had been a diplomat since 1977 and was a fluent Arabic and English speaker. He studied at Moscow Institute of International Relations and had been appointed as ambassador to Khartoum in 2013.
He previously served as ambassador to Rwanda, and had diplomatic postings in Egypt, Saudi Arabia and Yemen. A foreign ministry spokeswoman called him a “great professional”.
She added: “He dedicated his life to diplomacy. We express sincere condolences to his family and loved ones.” Six months ago, Russia’s ambassador to the United Nations Vitaly Churkin died after collapsing in his office in New York.
US officials have not disclosed the cause of Vitaly Churkin’s death, saying details were withheld to comply with international law. Russian officials argued that disclosing details could cause embarrassment to the ambassador’s family or hurt his reputation.
Mr Churkin, 64, reportedly became unwell and was taken to Columbia Presbyterian Hospital where he died on 20 February. In January Alexander Kadakin, Russia’s ambassador to India, died aged 68 from heart failure. And in December, Russia’s ambassador to Turkey Andrey Karlov was shot dead at an art exhibit in Ankara by a police officer.
Mr Karlov, 62, was giving a speech when off-duty officer Mevlut Mert Altintas entered the building and opened fire, before shouting: “Don’t forget Aleppo, don’t forget Syria!” He was killed apparently in protest at Russian involvement in Syria