The ship, thought to have been built in the late 18th or early 19th century, was found in the southern part of the lake at the depth of around 30 meters.
The vessel's hull, constructed without iron nails, is 16 m (52 feet) long, 5 m (16 feet) wide and 4 m (13 feet) deep. There is a hole in the right side of the hull and divers believe the ship sank during a storm.
They also discovered suspected human remains.
The expedition to the depths of the world's deepest and oldest lake was organized to search for historic artifacts linked with the Krugobaikal Railway, which saw numerous train crashes in the 19th century.
"We knew that this was the site of many train crashes and launched [the expedition] for this reason. As a result of the search, we ran across the sunken ship," Andrei Bobkov, a member of the diving team said, adding that the discovery was a complete surprise.
Bobkov said the team was also planning to make new dives to examine the ship and unearth the mystery of the shipwreck. However, the divers do not plan to recover the vessel due to concerns the wooden carcass, fragile after so long underwater, might be destroyed.
Baikal, called the Sacred Sea by locals for its size and beauty, is the world's oldest and deepest lake, with an age estimated at 25 million years. It holds around 20% of the planet's freshwater and is home to hundreds of unique species of fauna and flora.
The mysteries hidden in the lake's waters are currently attracting a great deal of attention. On Wednesday, a team of scientists using two Russian mini-submarines to research for the Russian Academy of Sciences, announced the completion of the first stage of their study.
The Mir-1 and Mir-2 deep-sea vehicles performed a series of 52 dives, including last week when they searched the lakebed for sacks of gold taken from the Imperial Russian reserves by the White Army's Admiral Alexander Kolchak when fleeing from the Bolsheviks in the winter of 1919-1920.
Some of the White Army officers reputedly froze on the ice as temperatures dropped to 60 degrees Celsius below zero, and the gold is thought to have sunk when the spring thaw came. However, no treasure, except boxes containing ammunition dating back to 1920s, was discovered.