http://news.bbc.co.uk/2/hi/south_asia/4368704.stm
The editor, Ali Mohaqiq Nasab, was convicted after a court in Kabul concluded that several articles in his magazine Huquq-e Zan were anti-Islamic.
Correspondents say the case underlines the fragility of journalistic freedom in post-Taleban Afghanistan.
It also highlights a struggle between religious moderates and extremists over what form Islam should take.
Mr Nasab was arrested earlier this month after he published a series of controversial articles.
One of them argued that giving up Islam was not a crime that should be punished by death, as sanctioned by some interpretations of Islamic Sharia law.
Other pieces criticised the practice of punishing adultery with 100 lashes and argued that men and women should be considered by Islamic law to be equals.
Clerics' ruling
The Ulema Council, a body of top Islamic clerics, reacted strongly against the articles.
"The Ulema Council sent us a letter saying that he should be punished so I sentenced him to two years' jail," Judge Ansarullah Mawizada told the Associated Press.
Mr Nasab said that he didn't recognise the court and did not accept its verdict.
The Afghanistan Independent Journalists Association has also spoken out against the verdict, saying it was outside the law.
"He wrote what he had the right to write according to Afghan law and press freedom and freedom of expression," the association's president, Rahimullah Samander, told AFP.
The New York-based Committee to Protect Journalists has called for his immediate release.
The editor has three weeks in which to appeal against the verdict.
In 2003, two journalists were arrested in Afghanistan over charges of defaming Islam.
They were later released on the orders of President Hamid Karzai.
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