On 2 February 2008, Darchinyan fought Z Gorres to a controversial split draw at the Waterfront Hotel in Cebu City, Philippines in an IBF Super Flyweight Eliminator where the winner would challenge the champion Dimitri Kirilov. The bout began with a knockdown for Darchinyan in the first round, which appeared to be a slip by Gorres when replayed. The crowd was upset with the referee calling the slip a knockdown and began to pelt the ring with bottles of water, coins and other objects. Gorres came back in the second round to floor Darchinyan with a left hand, but Darchinyan beat the count, which again prompted some arena fans to pelt the ring with objects. Gorres was knocked down in the fifth round, but the referee ruled it a slip. A clash of heads in the sixth round opened up a bad gash on Gorres. In the ninth round, Darchinyan connected with a right hand, sending Gorres down for the second time in the fight. Gorres would fall to the canvas on at least three other occasions in the final three rounds, with the referee ruling all of them slips. The final scores were 113–112 for Gorres, 114–112 for Darchinyan, and 113–113 for the draw. Darchinyan's promoter, Gary Shaw, filed an official protest with the IBF over the officiating of the bout.
Six months later, Darchinyan was back in what most experts called a career-best performance, taking on IBF super flyweight champion Dimitri Kirilov on 2 August 2008 at the Emerald Queen Casino in Tacoma Washington. Darchinyan dominated from the opening bell and showed an improvement in speed and boxing skill. He eventually caught Kirilov in round 5, dropping him twice en route to a round KO. Darchinyan was ahead 40-36 on all three judges' scorecards.
On 1 November 2008, Darchinyan fought WBC and WBA super flyweight champion Cristian Mijares at the Home Depot Center in Carson, California. Darchinyan was the aggressor from the outset, getting inside with big punches, including a left uppercut that knocked Mijares down in the first round. With his unorthodox crouching style, Darchinyan seemed to confuse Mijares, who was often content to counterpunch rather than attack. Mijares connected with just one combination the entire fight, that during a brief span of the fifth round. Darchinyan, however, was unhurt and unfazed. In the ninth round, Darchinyan caught Mijares with a right hand. Then as Mijares backed away, Darchinyan lunged and landed a straight left hand that knocked out Mijares. Darchinyan became the first man in history to unify the titles in the weight class.
On 21 September 2008, Darchinyan and fellow boxer Arthur Abraham were honored by Armenian President Serge Sargsyan during a 20th anniversary celebration of the nation's independence. Both men were awarded with medals "For the great services for Armenia" of the first degree.