The talks were held at Cyprus' initiative.
"They touched upon the regional problematic, including the situation in the Eastern Mediterranean and the prospects of the Cyprus dispute settlement," the Kremlin said in a statement.
The presidents also emphasized the need to "improve the contractual legal framework of the bilateral relations, including in finance and investment," the Kremlin added.
Putin and Anastasiades confirmed commitment to "further strengthen trade, economical and humanitarian ties between the two countries."
Earlier this week, the Turkish Foreign Ministry criticised a decision by the UN Security Council (UNSC) that extended the mandate of a peacekeeping force on Cyprus Island. According to the ministry, extending the mandate for six months without the consent of Turkish Cypriots is a violation of the rules and principles of the UN. The United Nations Peacekeeping Force in Cyprus (UNFICYP) has to make a legal arrangement with Turkish Cypriot authorities concerning its presence on the island, the ministry said.
The ministry added that Ankara has repeatedly stressed that issues related to the Eastern Mediterranean can be resolved through cooperation on hydrocarbon resources between Turkish and Greek Cypriots. Cyprus says that Turkey's drilling in the Eastern Mediterranean is a violation of its exclusive economic zones. The European Union is also concerned over the issue and has introduced sanctions against individuals and companies involved in the drilling. Turkey insists that the drilling serves the interests of the Turkish Cypriots who live in the north of the island.