Background <p>Genomic data sharing enhances efficiency in medical practice by facilitating faster data access and collaboration across settings. However, the same arrangements that enable efficiency could also raise legal inequalities, especially concerning data ownership and access. Yet these inequities are intensified in cross-border collaborations where power dynamics disadvantage low and middle income (LMIC) researchers.</p> Methods <p>A qualitative phenomenological study was conducted in Uganda. Key informant interviews (KIIs) were conducted with 49 stakeholders working at different points across the genomic research landscape and four focus group discussions (FGDs) were conducted with people currently or previously enrolled in genomic studies, or their caretakers. The stakeholders who took part in the KIIs included genomic researchers (16), research ethics committee (REC) members (14), practicing lawyers (3), community advisory board (CAB) members (8) and national research regulators (8). A theory of decolonization was used to clarify rooted power imbalances and unfairness. Through thematic analysis six concerns were identified: (1) inadequate regulatory frameworks, (2) limited access to the shared data, (3) unclear data ownership (4) absence of benefit sharing frameworks, (5) contested intellectual property rights and (6) rethinking power asymmetries and struggles.</p> Results <p>The wide spread perception by research participants that the Global North collaborators owned the data, eroded community trust. There was limited clarity on data ownership, with Ugandan researchers expressing differing views, on ownership, custodianship, and shared ownership leading to calls for co-ownership. In the absence of benefit-sharing frameworks to regulate the distribution of commercial value, data commercialization disadvantaged Ugandan researchers and participants, reinforcing colonial-like inequalities.</p> Conclusion <p>Current governance systems mirror colonial patterns in the control and sharing of genomic data in Uganda. These patterns are reinforced not only by cross-border power asymmetries but also by internal power dynamics within the country, including institutional hierarchies and regulatory gaps that limit local decision-making authority. Addressing this requires rethinking governance structures and promoting local or co-ownership models that reflect African interests and support decolonized approaches to data governance.</p> Trial registration <p>Not applicable. This study did not involve a clinical trial.</p>