While a lot of film studies look at how gay characters are portrayed or depicted in films, this study aims to identify various gay issues presented in select Philippine gay-themed films. Using critical discourse analysis, the two-fold objective in this paper is addressed by surfacing various gay issues presented in a mix of independent (indie) and mainstream films produced in the Philippines from 1998 to 2013. Gay issues in these films include themes on representation, acceptance, and rights and protection. After uncovering the issues and themes in these gay-themed films, the paper explicates the nuances of indie and mainstream films which could affect the selection of gay issues to be presented, how the issues are presented, and which audience or sectors are catered to. These nuances include differences in modes of production, use of technology, and production techniques. Overall, the political economy of media informs the study on the missing discourses about gay representation, identity and agency.