The human rights group also urged repeal of the "draconian" law used to imprison them.
The two men, identified only by first names -- Jonas, 19, and Francky, 20 -- were arrested in a car outside a nightclub July 25 in Yaounde, the capital of Cameroon.
Both have been charged under the country's penal code, which makes same-sex sexual acts a crime. If convicted, they could face up to five years in prison.
"Given the high level of officially sanctioned homophobia in Cameroon, those arrested under this law are at risk of attack or other forms of ill-treatment by fellow prisoners or by prison authorities because of their alleged sexual orientation," Erwin Van Der Borght, Amnesty International's Africa program director, said in a news release.
"By arresting people purely because of their alleged sexual orientation, the Cameroonian government is flagrantly violating international human rights treaties which it has signed or ratified."
The two men are the latest in a series imprisoned under the law, including Jean-Claude Roger Mbede, who was sentenced to 36 months in prison in March after sending text messages to a male acquaintance, Amnesty International said.
He is in Kondengui central prison, known for overcrowding, poor sanitation and inadequate food supplies, and is said to be in poor physical and mental health, and has been denied medical treatment, Amnesty International said.
The human rights group said it considers him a prisoner of conscience, imprisoned only because of his "real or perceived sexual orientation" and called on authorities to make sure he's not a victim of poor treatment, harassment or violence.
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