The visit at the invitation of President Dmitry Medvedev, due to last until Friday, comes 23 years after Ortega last visited Moscow in 1985, when he was first elected president of the Central American state.
The Kremlin said talks between the Russian and Nicaraguan leaders would focus on developing trade, Russia's Glonass satellite navigation system, space exploration, agricultural, transport and energy ties.
Nicaragua is a major exporter of coffee, nuts and tobacco to Russia. Russia's main exports consist of machinery, equipment and chemicals. Last year, Russian-Nicaraguan bilateral trade reached $6.8 million, and in the first nine months of 2008 hit $5.6 million.
"An exchange of views on the issues of bilateral cooperation at international and regional levels, processes in political and economic integration in Latin America and Russian membership to multilateral regional mechanisms will continue," the Kremlin said.
Nicaragua is the only country to back Russia in recognizing the breakaway regions of South Ossetia and Abkhazia as independent states following a brief Russian-Georgian conflict in August.
In a statement prior to Ortega's visit, the Kremlin said the two countries shared similar views on key issues on the international stage and called Nicaragua's decision to recognize the Georgian republics in September a "bright example."
Ortega, 63, enjoyed Soviet support in the 1980s after his Sandinista National Liberation Front overthrew the dictatorship of Anastasio Somoza in 1979. Ortega was elected president in 1985 and served until 1990. He returned to power after winning presidential elections in late 2006.
The Kremlin has recently moved to rebuild old alliances with Cuba and Nicaragua and cultivate ties with new countries such as Venezuela as part of Russian efforts to expand its global influence.
Russia's destroyer Admiral Chabanenko and two support vessels arrived in Nicaragua on Friday on a four-day visit delivering $150,000 in medical supplies, computers and other humanitarian aid.