But President Obama's Department of Justice appealed, and in 2015, the Ninth Circuit Court of Appeals ruled in the administration's favor.
She noted that Dwight Hammond is 76 and has served about three years in prison and that Steven Hammond is 49 and has served about four years.
"They now think they have a friend in the White House who does not value public lands", said Aaron Weiss, media director for the Center for Western Priorities, a nonprofit that advocates protecting public land.
The second imprisonment caused a local backlash.
The Hammond pardons have garnered attention from conservation groups calling Trump's action "dangerous".
The government said the ranchers were covering up evidence of hunting violations.
"Farm Bureau was shocked by the minimum five-year sentence the Hammonds faced", said American Farm Bureau President Zippy Duvall.
The Malheur 7, as they came to be known, were later acquitted of the government's charges by a jury.
The nonprofit would not have objected to Trump simply commuting the Hammonds' sentences and setting them free, Weiss said.
The decision sparked a protest from Ammon Bundy and dozens of others, who occupied the Malheur National Wildlife Refuge near the Hammond ranch in southeastern OR from January 2 to February 11, 2016.
In its statement Tuesday, the White House called the appeal "overzealous" and the resulting sentence "unjust".
The move by Trump raised concerns that others would be encouraged to actively oppose federal control of public land. "Justice is overdue for Dwight and Steven Hammond, both of whom are entirely deserving of these grants of executive clemency".
"The 2001 blaze burned 139 acres of public land, according to court documents; the 2006 fire - for which only Steven was convicted - burned an additional acre of public land".
The U.S. Attorney's Office in OR said Astarita falsely stated he had not fired his weapon during the attempted arrest of protester LaVoy Finicum, who was shot dead by another officer during the incident, "when he knew he had in fact fired his weapon".
"We think this sends a very risky message that will put America's park rangers, law enforcement officers and public land managers at risk", he said.
Trump has often used his pardon power to benefit people he sees as targeted by his political opponents.
The Oregon Farm Bureau said in a statement "while nobody can restore what they've lost to this prosecutorial overreach and bureaucratic vendetta, we are happy that this very bad chapter will be coming to a close soon".
A White House statement released Tuesday announced the pardons for both Hammonds, stating they were "imprisoned in connection with a fire that leaked onto a small portion of neighboring public grazing land".