Last week the court ruled that the husband was, in fact, a woman, despite sex-change surgery and that the couple had lied about his sexual status.
It also said that their marriage is un-Islamic because it of the same-sex.
The court has also directed the police to trace the surgeons who carried out the sex change operation. The court will decide next month whether to annul the couple's marriage.
Shumail Raj, 31, had sex-change surgery to become a man and then married his cousin who was aware of the condition but says she needed his help to avoid being forced into wedlock with someone else.
He is reported to have undergone surgery twice in Pakistan over the past 16 years to become a man. But tests carried out by doctors on behalf of the court ruled that Raj is still a woman.
Reports said Raj and his 24-year-old wife Shahzina Tariq appeared shocked by the verdict.
"We appeal to President Musharraf to intervene. Musharraf is talking about moderation and enlightenment. We hope he will do something for us," Raj said.
Meanwhile, Shahzina also said that they are not homosexuals and they married because they are in love.
The two were arrested a fortnight ago after the bride's family complained about the gender of her husband.
Source: IBN