The charges carry penalties of up to 14 years in prison. Prosecutors said they might bring additional charges.
The two men were arrested Sunday after performing a traditional wedding ceremony before hundreds of curious onlookers.
The Center for the Development of People, which fights for the rights of gays, prostitutes and prisoners, said it would support the men’s defense. It said the laws used to arrest them are invalid because they run counter to the Bill of Rights in Malawi’s constitution.
But the Malawi Law Society urged authorities to prosecute calling the wedding illegal and against the order of nature.
The head of the Center for Human Rights and Rehabilitation, Undule Mwakasungura, agreed that the men had violated Malawian law. But he said society could not continue to pretend that gays do not exist.
"The challenge is that gays and homosexuals are part and parcel of us as Malawians, as Africans," said Mwakasungura. "We cannot continue discriminating against them."
Pearson Mtata is a sociology professor at the University of Malawi who has researched homosexuality in Malawi. He told national radio that African gays face a dilemma because traditional values are still strong.
"Most of them [gays] are afraid to come out, not because they are ashamed of their behavior but because they are afraid of society," said Mtata.
Homosexuality is considered taboo in most traditional African societies and is illegal in most African countries.
Senegal recently arrested 25 men at a party and charged them with committing indecent acts. Uganda is soon to debate a law proposing the death penalty for some gays.
South Africa has legalized same-sex marriage and its constitution guarantees the rights of gays and lesbians. But traditional and religious members of parliament have proposed amendments outlawing same-sex marriages.
Mwakasungura believes one of the reasons for the public wedding ceremony was to challenge these laws and customs.
"This has given us a wake-up call but also a new chapter in terms of how we deepen the discussion or the debate on the gay citizens in Malawi," he said.
He notes that the country’s law commission is examining outdated laws and could look at same-sex marriages.