Climate change poses significant challenges to coastal communities in Southeast Asia, where fisheries are not only vital for food security and livelihoods but are also deeply gendered. Women play essential roles across the fisheries value chain, yet their contributions and vulnerabilities remain largely invisible in policy frameworks. Here, we analysed the extent of gender integration in fisheries and climate policies (n = 115) in Indonesia and the Philippines – two countries with high female participation in fisheries and significant climate vulnerability. Our findings reveal a greater level of gender integration in the Philippines, particularly at higher governance levels, with Indonesia’s efforts to mainstream gender at a nascent stage. However, both countries lack actionable strategies and resource allocation to operationalize gender commitments at local levels. Policies also represent gender equality as a women’s issue and primarily portray women as homogeneously vulnerable, overlooking intersecting identities and local contexts. This approach has led to gender strategies that focus on institutional structures or women as beneficiaries, with limited attention paid to gender dimensions at a community level. Our results emphasise the need to strengthen implementation mechanisms at local levels, embed intersectional perspectives, and improve coordination between governance levels and sectors to support gender-responsive and inclusive climate adaptation in the fisheries sector.