The conservation of migratory species can be problematic because of their requirements for large protected areas. We investigated this issue by examining the annual movements of the migratory wildebeest, Connochaetes taurinus, in the 25000 km2 Serengeti-Mara Ecosystem of Tanzania and Kenya. We used Global Positioning System telemetry to track eight wildebeest during 1999–2000 in relation to protected area status in different parts of the ecosystem. The collared wildebeest spent 90% of their time within well-protected core areas. However, two sections of the wildebeest migration route – the Ikoma Open Area and the Mara Group Ranches – currently receive limited protection and are threatened by poaching or agriculture. Comparison of current wildebeest migration routes to those recorded during 1971–73 indicates that the western buffer zones appear to be used more extensively than in the past. This tentative conclusion has important repercussions for management and needs further study. The current development of community-run Wildlife Management Areas as additional buffer zones around the Serengeti represents an important step in the conservation of this UNESCO World Heritage Site. This study demonstrates that detailed knowledge of movement of migratory species is required to plan effective conservation action.