A History of Claims and Tensions

The relationship between Kenya and Uganda has been marked by periods of both cooperation and significant tension since independence. Historical flashpoints include Ugandan dictator Idi Amin's 1970s claim to Kenyan territory stretching to Naivasha, a threat that was met with a firm military warning from President Jomo Kenyatta. More direct conflict erupted between 1987 and 1990 under Presidents Daniel arap Moi and Yoweri Museveni, fueled by mutual suspicion and accusations of supporting rebel movements against each other. This period saw military skirmishes at the Busia border town and even the bombing of Lokichogio by the Ugandan air force, bringing the two nations to the brink of war before a peace deal was brokered in August 1990.

In recent years, the most persistent source of friction has been the dispute over the tiny, fish-rich Migingo Island in Lake Victoria. The island, inhabited mostly by Kenyan fishermen, has been a point of contention with Ugandan security forces periodically occupying it and harassing Kenyan citizens. Despite numerous high-level discussions and agreements aimed at resolving the dispute, including a 2009 pact to survey the border based on a 1926 colonial accord, the issue remains a potent symbol of the underlying border tensions.

New Rhetoric and its Implications for Kenya

The latest source of concern stems from recent remarks by President Museveni, who, in a televised address on November 14, 2025, declared, “The Indian Ocean is mine. I'm entitled to that ocean.” While some analysts have interpreted this as metaphorical rhetoric born of frustration over Uganda's landlocked status, it has nonetheless caused alarm in Kenya, reviving memories of past territorial claims. Uganda is heavily dependent on Kenya's Mombasa port for its imports and exports, a strategic vulnerability that has been a recurring theme in bilateral relations. This dependency has led to trade disputes, most notably in late 2023 and early 2024 when Uganda sued Kenya at the East African Court of Justice over restrictions on its state oil company importing fuel directly through Mombasa.

President Museveni's comments are seen by some as a tactic to rally domestic support ahead of Uganda's 2026 elections and project strength regionally. However, they come at a sensitive time. In November 2025, fresh allegations surfaced from Kenyan activist Bob Njagi, who claimed that Ugandan soldiers, disguised as Kenyan police, were deployed to help suppress the 2024 'Gen Z' protests in Kenya. These claims, coupled with the 38-day detention of Njagi and another activist in Uganda, have introduced a new and troubling dimension to the relationship, suggesting a level of security cooperation in internal affairs that has alarmed human rights organizations.

Economic Interdependence and the Path Forward

Despite the political friction, Kenya and Uganda share a deep and vital economic partnership. Uganda is one of Kenya's most significant trading partners, and any instability has immediate and severe consequences for cross-border commerce. Disruptions at the border, whether from political disputes or protests, can cripple supply chains, increase transport costs, and lead to shortages of essential goods like fuel in Uganda. This economic reality often forces a pragmatic approach to resolving disputes. For instance, following President Museveni's state visit to Kenya in July 2025, the two countries announced an agreement to remove trade barriers and ease the movement of goods and people.

The East African Community (EAC) continues to play a role in mediating these tensions. Initiatives like the EAC Peace Caravan, launched in mid-2023, aim to promote dialogue and resolve disputes among border communities, particularly in the volatile Karamoja cluster, which has historically seen conflict over resources like water and pasture. However, the effectiveness of these regional mechanisms is tested by the unilateral actions and rhetoric of member states. As Nairobi navigates this latest challenge, it must balance the need to firmly defend its territorial integrity with the economic necessity of maintaining a stable relationship with its most crucial regional partner. The coming months will be critical in determining whether the echoes of past tensions escalate into a new crisis or are managed through renewed diplomatic engagement.