For centuries, South Asia has had its own Khawaja Sira or third gender culture. The community, identifying as neither male nor female, are believed by many to be "God’s chosen people," with special powers to bless and curse anyone they choose.

The acceptance of Khawaja Sira people in Pakistan has been held up internationally as a symbol of tolerance, established long before Europe and America had even the slightest semblance of a transgender rights movement.

But the acceptance of people defining their own gender in Pakistan is much more complicated. The term transgender refers to someone whose gender identify differs from their birth sex. This notion is yet to take root in Pakistan and the transgender rights movement is only beginning to assert itself formally. Now, some third gender people in Pakistan say the modern transgender identity is threatening their ancient third gender culture.

Kami Choudary has made international headlines and has been billed as "Pakistan’s first transgender supermodel." This year Choudary delivered her first TEDx talk and she makes regular speaking appearances, telling her story and debating transgender rights in university auditoriums. She asserts herself, not as a Khawaja Sira but as a transgender woman. She acknowledges that her experience, as a rising transgender celebrity in Pakistan, is not the norm.

“My mother supports me. My boyfriend supports me and my mentors and friends support me,” says Kami, who wants transgender people in Pakistan to be more vocal. “We have to do something. I am very public so people are always talking about Kami.”

Choudary benefits from the privilege of familial support and being able to identify as she chooses. She is educated, English speaking and from a fairly affluent family. In contrast, many Khawaja Siras are disowned by their biological families. The community is discriminated against heavily, with most Khawaja Siras making a living from performance, sex work or begging. They are simultaneously celebrated as "gifted" by God and ridiculed for not conforming to the male/female gender roles that society prescribes.

Bindiya Rana is the grand matriarch of the third gender community in Karachi. She doesn’t prescribe to the transgender identity. She is a Khawaja Sira, so revered that she is a guru (teacher) to more than 50 chelahs or apprentices.

This relationship has a parental element and is a cornerstone of Khawaja Sira culture. Each chelah pledges allegiance to their guru, as they did to their guru before them. These family trees provide acceptance, social support and financial backing. Most chelahs give a percentage of their income to their gurus. It’s a lifetime commitment that allows the establishment of families that often replaces biological lineage.

But those who identify as transgender, like Choudary, don’t subscribe to the guru-chelah system. As a result, Rana and her chelahs view the transgender identity as alien and even immoral.

“If you don’t have a guru, we don’t recognize you. These people who say they are transgender; that concept is just wrong," says one of Rana's chelahs. "They can never be women. They cannot give birth. Even if they change their bodies they can’t change who they are. We are not women. We are what Allah has made.”

Such sentiment detracts from the idea that Pakistan has a liberal take on transgender rights. It’s more accurate to assert that Pakistan has an established acceptance of third gender culture. These are two different things.

The clash between transgender women and third gender Khawaja Siras can be characterized by differences in education, language and age. Increasingly, young Pakistanis who don’t identify with the gender assigned to them at birth assert themselves as transgender and not Khawaja Sira.

Qasim Iqbal coordinates research into gender and sexuality for the Naz Project in Pakistan. In a survey conducted in 2011, participants where asked if they identified as male or female. Eighty-seven percent of those questioned said they identified as neither and preferred instead the term third gender. But Iqbal suggests this is now changing.

“When the newer generation say they are transgender they are referring to the transgender that the West acknowledges. A lot of the modern transgender women are wearing Daisy Duke shorts and tube tops. They are breaking away from the tradition. They are becoming more hip and modern," says Iqbal.

Even if Khawaja Siras and transgender women identify differently and prescribe to different cultures, the longstanding acceptance of the Khawaja Sira culture in mainstream Pakistan offers transgender women an umbrella of protection. The idea of boys growing up to identify as Khawaja Sira rather than the gender assigned to them at birth, is nothing new in Pakistan. It is accepted — in varying degrees — in every Pakistani village, town and city.

But what if you identify not as a Khawaja Sira, or even as a transgender woman, but as a transgender man? In Pakistan’s fiercely patriarchal society, the idea of a person whose birth sex is assigned as female growing up to identify as male is almost unheard of.

In Lahore, Mani and girlfriend Razia have worked hard to establish a home together. Mani is a transgender man and is very clearly in love. While looking at Razia, he says, “She is a perfect girl. She is a marriage material woman so I can’t see my life without her.”

The couple eloped from their native Karachi to live and love as they have chosen. But there has been a price to pay.

“My dad said, ‘If you go to Lahore, I will not talk to you again.’”

Mani now has no relationship with his father although he does speak to his mother and siblings regularly. In a society where relationships are so often public property, leaving home to live with a lover and identifying as a transgender man are both revolutionary acts.

Mani recently had a double mastectomy and plans on ovary removal in the coming year.

“I think I am the first transgender man in Pakistan to have this breast removal surgery. I am on hormones. The ovary removal is expensive and we don’t have facilities in Pakistan, so it will take some time,” he says.

Mani has contacted other transgender men in Pakistan and he believes the community is slowly, becoming more visible.

In its 70th year of independence, the discussion of gender in Pakistan is more complicated than it’s ever been. In some ways, Pakistan is years ahead of Europe, acknowledging and sometimes celebrating a third gender as part of its established history and future. But the ability to choose gender identity outside of the established third gender system remains elusive and is almost exclusively the preserve of an affluent, educated minority.

Mobeen Azhar's BBC radio documentary Inside Transgender Pakistan is available to download and stream.

Follow Mobeen at @Mobeen_Azhar