Rickie Fowler, 28, was indicted on five counts of murder, one count of aggravated arson and one count of arson of an inhabited structure, San Bernardino County District Attorney Michael Ramos said.
Ramos said hundreds of people lost their homes, including some prosecutors on his staff.
"Our hearts go out to the thousands of people who were affected by this," he said. "Although justice was delayed I will tell you justice will not be denied in this case."
Fowler, imprisoned on a theft conviction, was interviewed in connection with the fire in February 2004 based on a telephone tip, but there was not enough evidence, Deputy District Attorney Vic Stull said.
The investigation began to gain steam in February 2008 and new evidence was obtained as recently as three weeks ago that allowed prosecutors to identify Fowler as a suspect, Stull said.
Another man, Martin Valdez Jr., was also believed to be a suspect but he was shot and killed in Muscoy in 2006.
Stull said prosecutors were not sure who actually threw a road flare that started the blaze but are confident they have enough evidence.
The statute of limitations on arson would have run out on Oct. 25, Stull said.
Prosecutors have not determined whether they would seek the death penalty if Fowler is convicted, Stull said. Fowler's arraignment is expected within two weeks, after he is transferred from a prison in Lancaster.
The notorious Old Fire was part of a siege of wildfires that year that scorched hundreds of thousands of square miles and burned thousands of homes, forcing residents to flee across a broad swath of the region.
The fire erupted in the Waterman Canyon area of the San Bernardino Mountains above the city of San Bernardino and eventually swept across 90,000 acres, or about 140 square miles.
Although authorities initially linked six fatal heart attacks to the distress of the evacuations, Stull said in one of those cases the victim's widow felt that the attack was not caused by the fire.
Several witnesses reported seeing a passenger in a white van tossing burning objects into dry brush. In late 2004 San Bernardino County authorities said they were focusing on a young man they believed may have been the arsonist and were trying to identify a second man but did not have enough evidence to make arrests.
Stull said neither Fowler nor the other man owned the white van, but he alleged that they had borrowed it. The actual owner was unaware of its involvement.
On Dec. 25, 2003, 14 people were killed when several inches rain sent a massive flow of debris-laden runoff rushing down the barren slopes of Waterman Canyon, sweeping away a church camp. Two other people died that day in a debris flow in another fire area.
Stull said murder charges were not possible in the flood deaths because months had elapsed since the fire and there were too many other variables.
The indictment in the Old Fire is the latest effort to solve arson crimes behind destructive and deadly wildfires that plague Southern California, especially in the fall as seasonal Santa Ana winds blow.
On Monday, Los Angeles County authorities charged a homeless man with igniting a tiny August blaze close to where another wildfire broke out several days later and eventually burned over 250 square miles.
Authorities have not called Babatunsin Olukunle, 25, a suspect in the gigantic Station Fire northeast of Los Angeles but have referred to him as the "best lead" in the case. He pleaded not guilty at his arraignment.
The Station Fire probe is also a homicide investigation because two firefighters were killed when their vehicle plunged off a mountain road as the blaze approached an inmate firefighting camp.
Four months ago, a Riverside County man was sentenced to death for setting an October 2006 wildfire that killed five U.S. Forest Service firefighters who were trying to defend a remote home in the San Jacinto Mountains as Santa Anas whipped up a firestorm.
In that case, Raymond Lee Oyler, 38, was convicted of five counts of first-degree murder. He is believed to be the first person sentenced to death in the U.S. for an arson wildfire involving the deaths of firefighters.