The High Court in Dhaka dismissed a legal challenge from a father whose son married a Rohingya teenager in a Muslim ceremony in September despite laws forbidding such unions.
Marriages with Rohingya were banned in 2014 to try to prevent hundreds of thousands of refugees living in Bangladesh from seeking a back door to citizenship.
Babul Hossain, whose 26-year-old son ran away with his new wife after they married, questioned the legality of the ruling that threatens a seven-year jail term for any Bangladeshi who weds a Rohingya refugee.
"The court rejected the petition and has upheld the administrative order, which bans marriage between Bangladeshi citizens and Rohingya people," deputy attorney general Motaher Hossain Saju told AFP.
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Hossain's request that the court protect his son from arrest was also rejected, Saju added.
About 655,000 Rohingya have escaped to Bangladesh since August after the Myanmar army began a campaign of rape and murder in Rakhine state.
They joined the more than 200,000 refugees already living in Bangladesh who had fled previous violence in Rakhine.
Hossain could not be contacted after the ruling.
But in a previous statement, he defended his son's marriage to the 18-year-old Rohingya woman and denied it was driven by a quest for citizenship.
"If Bangladeshis can marry Christians and people of other religions, what's wrong in my son's marriage to a Rohingya?" Hossain told AFP.
"He married a Muslim who took shelter in Bangladesh.