The commission said that the fungus-like disease has been confirmed in larches in two woodlands, one in West Sussex and the other in Surrey.
Ramorum disease has been responsible for the premature felling of more than 3 million larch trees in the United Kingdom since it was first found killing larches in the West Country in 2009.
Alison Field, South East England director for the Forestry Commission, said: "Like all phytophthora organisms, P. ramorum thrives in the kind of wet weather we have had this year.
"It is also significant that both of the affected woodlands are close to areas where rhododendron shrubs have been infected with P. ramorum as well, so although this is bitterly disappointing news, it is understandable that it has spread into local larch trees."
She said that the only treatment to stop the spread of the disease was to fell infected trees before they can produce spores.
The Forestry Commission first became concerned when larch trees showing symptoms were spotted during a helicopter survey of the region in June, and ground-based checks confirmed the surveyors' suspicions.
Most previous cases have occurred in the wetter, western parts of Great Britain as well as Northern Ireland, the Republic of Ireland and the Isle of Man.
The Forestry Commission has issued statutory "plant health notices" to the affected owners, requiring them to fell the infected larch trees and others nearby.
Field said: "I would urge all woodland owners in the South East to inspect their trees regularly for signs of ill health, and to report anything suspicious.
"Those who have rhododendron plants in their woods or gardens should keep a close eye on them too, because infected rhododendron can also produce millions of the spores which spread the disease."