Indonesia has a long history of a third gender known as “waria,” that today is often compared to being transgender. Is there a similar historic precedent for male-male or female-female romantic/sexual expression in early Indonesian cultures?

I have an earlier answer on trans history in Southeast Asia, that also goes into "same-sex" relations:

According to scholars like Michael Peletz and Tamara Loos, shared geographic/climatological context and millennia of contact among themselves and with “fringe” states (India, China, Japan) have led to a certain porousness of cultural features even amidst awesome diversity. Practices of and attitudes towards gender pluralism are one of the most interesting areas to compare and contrast.

Peletz discusses gender pluralism in southeast Asian societies in several successive stages: pre/early-European contact (through the early 20th century); the era of state formation and European colonialism (18th-20th centuries); and globalization/entrenchment of capitalism and European-style modernity (mid-20th century).

For the earliest stage, it’s important to be aware, many of his sources are 19th/early 20th-century European travelers and ethnographers. (There is additional material from several of the states and Portuguese, especially, explorers going back to the 14th and 16th centuries respectively). However, through comparisions among societies and by examining both change and continuity over the late 19th to mid-20th century sources, Peletz says he is confident that he can discuss genuinely “early modern” gender pluralism.

The most important clarification to make is that we are primarily talking about gender here, not sexuality or sexual orientation. Tamara Loos makes this point much more strongly than Peletz, but I think it’s an important one. The early modern and modern West foregrounds sexuality and emphasizes hetero-sexual relations as the central axis of gender/sexuality; early modern Southeast Asian societies focused on hetero-gender (and cisgender) lifestyle and relationships.

In early modern Southeast Asian societies, ideas of gender arose out of/with a cosmological concept of the gendered sacred: the divine encompassed both female and male (and agender, in some origin myths). That is to say, there was real power in both female and male/femininity and masculinity. Our information about gender pluralism comes mostly from a religious context, in fact.

The Bugis of South Sulawesi provide the best-known example of the most common form of gender pluralism. One class of their sacral priesthood is called the bissu. In the early modern era—it’s attested by both Sulawesi and Portuguese sources from the 16th century on—the bissu included normatively gendered female-assigned priests as well as male-assigned priests who reassigned themselves as cisgender female.

In a hybrid local belief system with elements of Islam, Buddhism, and indigenous Austronesian religion, the bissu served as royal priests and guardians of their sacred texts. Transgender bissu adopted normatively-female clothing and mannerisms. They also set themselves up as women in society—most critically, as wives. European writers made the immediate leap to sex, denouncing the trans bissu as sodomites.

My point here isn’t to say whether or not homo-sexual relationships occurred in any given hetero-gender couple; the point is that for the early modern Bugis, that question was, well, beside the point.

While the bissu and their counterparts were permanent, lifelong transitions, it’s interesting to observe temporary transgender adoption as well. In 19th century Aceh, there were competitions of religious and literary knowledge between teams from mosques and madrasas from neighboring villages. A key player on each team was the sadati--a “dancing boy” who adopted the dress and manner of a young woman for the course of the contest.

European ethnographers documented homo-sexual relations among the members of a given team; interestingly, this included both homo-gender and hetero-gender relationships.

I’ve concentrated on the Bugis out of Peletz’s examples because there is also documented, accepted gender-crossing outside a religious context. Both calabai (men reassigned as women) and—somewhat unusually--calalai (women reassigned as men) crossed the gender boundary for the duration of their lives. Grandiose-minded imperialist James Brook in 1848 noted:

The strangest custom I observed is, that some men dress like women, and some women like men; not occasionally, but all their lives, devoting themselves to the occupations and pursuits of their adopted sex. In the case of the males, it seems that the parents of a boy, upon perceiving in him certain effeminacies of habit and appearance, are induced thereby to present him to one of the rajahs, by whom he is received.

The really interesting thing to me is that despite the insinuations we might read into this, Brook is careful to distance this gender transgression from sexual transgression: becoming a calabai does not mean one engages in homosexual behavior. Now, he’s making a point about what he sees as the horrors of the Ottoman Empire as much as promoting the Bugis here, so I’m not sure how far we should take that part at face value.

What’s more interesting, especially given the existence of calalai as well as calabai, is Brooks’ recognition of an overall good status for women in Bugis society. He is particularly impressed by women’s roles in government and the lack of prostitution.

Our self-appointed white rajah (no, really) isn’t the only one concerned with prostitution in relation to gender and gender pluralism. In the later chapters of his book, Peletz turns to the reasons for Southeast Asia’s mid-20th century shift towards opprobrium against homosexuality that partially brought gender-crossing down with it.

One of the biggest causes he finds is a marked drop in the status of women and femininity. The commodification of sex into prostitution, including through Western military presence and sex tourism, might give some individual women a sense of empowerment over their own circumstances but has overall helped drive the objectification of women. While the bissu and counterparts found increased sacred power in blending their born-maleness with lived-femaleness, the power of femaleness declined markedly.

The changing role of religion in Austronesian and peninsular societies, too, has played a factor. The more organic and cosmological rooting of spirituality has been overwritten by the “rationalization” of beliefs (expressed as doctrine/facts to learn).

And finally, as in the West, political centralization, state formation, and the rise of capitalism were powered by the drive for rigidity, order, social stratification, normativity.

But most important, Peletz stresses, these processes have by no means been complete. The work of individual activists as well as the dyed-in inheritance from centuries or millennia of gender pluralism have helped modern southeast Asian cultures maintain at least an ambivalence towards trans people and culture in the face of military dictatorship, outside imperialism, and religious fundamentalism.