Vessels linked to Russia’s largest grain trader shipped thousands of tons of stolen Ukrainian grain to global buyers, using a sophisticated system of feeder vessels and floating cranes, according to an investigation by The Wall Street Journal.

The ships are linked either through their management or ownership to companies controlled by Russian businessman Peter Khodykin, who in turn owns RIF Trading House LLC, the country’s largest grain exporter and a big player in global grain markets, according to corporate and legal documents reviewed by the Journal.

The Journal has previously reported widespread theft of grain and land in Russian-occupied Ukraine, including detailing an intricate system by which smugglers clandestinely trucked out large amounts of stolen grain from newly occupied farms in eastern Ukraine to Crimea, which Russia annexed in 2014.

The next step in the smuggling process: moving that stolen Ukrainian grain from Crimea to global buyers. A fleet of small vessels ferry smuggled grain, typically from the Crimean port of Sevastopol, to larger cargo ships waiting at sea, where they transfer their cargo with the help of crane-equipped vessels, according to the Journal’s investigation. Those larger ships then set sail for far-flung ports.

Such at-sea transfers can hide the true provenance of the ships’ cargoes, which buyers might shun if they suspected the grain came from Russia-occupied eastern Ukraine. The transfers allow big container ships, which can be easily recognized in port or from satellite imagery, to avoid calling at Sevastopol. Sometimes the stolen Ukrainian grain is mixed with Russian grain, to further disguise the cargo’s origins.

“It’s wheat laundering,” said Yoruk Isik, head of the Istanbul-based Bosphorus Observer, an independent ship-tracking consulting firm. “They made it really hard to track.”

June 5: Ship-tracking data show the Emmakris II, a large bulk carrier, arriving in the Black Sea, having sailed from Saudi Arabia. The M. Andreev, a small feeder ship, meanwhile, had been operating in the days before around the Kerch Strait.

June 11: A few days later, Petra II, a crane ship, is captured by satellite imagery sandwiched between the Emmakris II and a different feeder ship. Ukrainian intelligence and maritime experts say it was loading grain at sea.

June 14: Ship-tracking data and satellite imagery show the M. Andreev, the Emmakris II and the Petra II operating in the vicinity of the Kerch Strait. Ukraine intelligence say the M. Andreev was loaded with barley from Sevastopol.

TURKEY, RUSSIA REACH FRAMEWORK ON SHIPPING UKRAINIAN WHEAT THIS MONTH: EXCLUSIVE

June 15: Ship-tracking data showed the three ships alongside each other for seven hours. Here, the barley was loaded from the M. Andreev, according to maritime experts and Ukrainian intelligence. Satellite imagery then picks up the M. Andreev breaking off.

Sept. 4: The Emmakris II lists its intended port of destination in Iraq, after sailing from the Kerch Strait through the Bosporus and Suez Canal. It never recorded a port call.

Ukrainian authorities and maritime and grain-market analysts have identified Sevastopol as a key entrepôt for stolen grain brought in by truck or rail from eastern Ukraine. Sevastopol shipped about 848,400 tons of grains, such as wheat and barley, from the beginning of March through October, nearly 15 times as much as the same period last year, according to Geneva-based researcher AgFlow.

In one such at-sea transfer of cargo coming from the port this summer, a crane ship managed and owned by companies linked to Mr. Khodykin loaded a large cargo ship—also managed and owned by the same companies—with grain near the Kerch Strait, a narrow waterway connecting the Black Sea and the Azov Sea, according to Ukrainian intelligence reports, satellite imagery, shipping data and maritime analysts.

Mr. Isik’s Bosphorus Observer helped identify some of the ships involved in Kerch Strait smuggling by matching verified photos and video with satellite imagery, using characteristics such as the placement of cranes and hatches on the ships. The Initiative for the Study of Russian Piracy, a Washington-based group of researchers and former U.S. officials funded by a Ukrainian industrial group, also provided ship-tracking data and corporate documentation. The data and documents were corroborated by the Journal.

Mr. Khodykin couldn’t be reached for comment. RIF said it has nothing to do with Ukrainian grain theft. “We value our reputation and comply with the legislation of the Russian Federation and all international rules,” the company said via email. RIF said that it carefully checks the origin of all its cargoes. Russian officials have also denied the theft of Ukrainian grain.

RIF, based in the city of Rostov-on-Don on the Azov Sea, is Russia’s largest exporter of grain, according to the country’s main grain trade body. According to Russian corporate documents dated as recently as April this year, Mr. Khodykin is RIF’s owner.

From April to September, Sevastopol shipped 662,000 tons of grain, compared with 36,000 tons the year before, according to AgFlow. Companies controlled by or benefiting Mr. Khodykin were involved in about a third of this year’s excess exports, according to ISRP researchers. That estimate took into account ISRP-tracked bulk carriers, tugboats, cranes and other auxiliary ships owned or managed by companies linked to Mr. Khodykin that either delivered grain or assisted in transshipments.

For instance, on June 14, the Russian-flagged M. Andreev, a small feeder ship, arrived in the vicinity of the Kerch Strait, loaded with barley from Sevastopol, according to a Ukrainian intelligence document. Near the strait, it came alongside the Panama-flagged Emmakris II, which had arrived earlier in the month, according to ship-tracking data from Spire Global.

The Emmakris II has been managed since 2020 by Dubai-based MCF Shipping DMCC, according to Equasis, a shipping database. It is listed as owned by an affiliate of MCF Shipping. MCF Shipping, in turn, shares a corporate website registrant and administrator with GTCS Trading DMCC, another Dubai company that a 2019 Moscow arbitration court document identified as being beneficially owned by RIF’s Mr. Khodykin. The company also goes by GTCS Trading JLT.

MCF Shipping is located in a Dubai office building next to GTCS Trading. Employees of the two companies say on their LinkedIn profiles that they work for both companies. One employee of GTCS reached by phone by the Journal said the two companies were the same. GTCS was also the majority owner of RIF until April this year, when ownership changed to Mr. Khodykin, according to a database that aggregates information about Russian companies.

On June 15, both ships, the Emmakris II and the M. Andreev, appeared on ship-tracking sites next to each other, along with another ship with a mounted crane. The three ships were nestled together for more than seven hours, according to ship-tracking data and a Ukrainian intelligence document, which said the M. Andreev offloaded its grain at this point.

The crane ship, Petra II, is also managed by MCF Shipping, the Dubai-based company linked to Mr. Khodykin, according to the Equasis shipping database. It is owned by an affiliate of MCF Shipping.

The flotilla was joined by two more feeder ships, this time arriving from Russia. They moored alongside the Emmakris II, according to satellite images from Planet Labs PBC that were reviewed by the Journal. Ukrainian officials say Russia mixes Russian grain with stolen Ukrainian grain to make it harder to track.

Emmakris II then got under way, moving first into the Black Sea and then through the Bosporus on July 10, according to ship-tracking data from Spire Global.

The ship then sailed to the Persian Gulf, where its tracking transponder stopped transmitting, making it invisible to ship trackers. When the ship reappeared on Sept. 4, it listed its destination as Umm Qasr, Iraq. The ship never recorded a port call in Iraq, however, according to ship-tracking data. Its final destination on that voyage couldn’t be determined.

Since September, the Emmakris II has made two more trips through the Black Sea to the Kerch Strait, according to ship-tracking data. The ship returned to the Persian Gulf on the first of those trips. The ship left the Black Sea again earlier in November and transited the Suez Canal on its way to the Red Sea.