The burnt bodies of the victims, including a park ranger known for his fight against poaching, were found in the Ile-Alatau national park in late August. They had been stabbed to death.
Police identified the suspects as Sayan Khairov and Zaurbek Botabayev, born in 1975 and 1978 respectively. They did not identify the organization the two allegedly belong to, describing it only as an "extremist religious group."
The Interior Ministry said in a statement the two suspects are also suspected of involvement in an explosion at a house on the outskirts of Almaty in July where seven people died.
Kazakhstan, a sprawling mainly Muslim former Soviet nation west of China, saw a surge last year in terrorist activity apparently linked to Islamist extremism. Several attacks have been reported over the summer after a largely quiet first half of the year.
Dozens have died, mainly suspected terrorists and law enforcement officers, since an unprecedented suicide bombing in May 2011 in the western city of Aktobe.
No clear motivation has emerged for the unrest. Signs of religious extremism are unusual for a country in which most Muslims practice a moderate strain of the faith.
The bulk of clashes have been centered in the west near the country's
It is unclear whether alleged militant groups linked to attacks in and around Almaty are operating in concert with militants in the west.