Radio telemetry was used to determine the distribution, locate spawning sites, and evaluate the tagging response of wild Chinook salmon Oncorhynchus tshawytscha returning to a large, free-flowing river basin. A total of 2,860 fish were radio tagged in the lower Yukon River and tracked upriver. Fish traveled to spawning areas throughout the basin, ranging from several hundred to over 3,000 km from the tagging site. We found similar distribution patterns across years, suggesting that the major components of the return were identified. Most spawning fish were clustered in a number of principal tributaries, although small numbers of fish were located in other spatially-isolated areas. The cumulative contribution of these minor stocks was appreciable, making up 28-31% of the tagged sample. There was suggestive evidence of mainstem spawning in upper reaches of the basin. Large-scale elevation and physiographic data were useful in categorizing spawning areas, with most fish returning to relatively entrenched upland rivers. Fish were largely absent in lowland reaches characterized by meandering, low gradient, alluvial channels often associated with main river floodplains. The fish generally responded well to the capture, handling, and tagging procedures with most (2,790, 97.6%) resuming upriver movements, although the fish initially displayed a negative tagging response, with slower migration rates observed immediately after release. The duration of this response was relatively short (several days) and less severe as the fish moved upriver. The swimming speeds of radio-tagged fish after the initial delay were comparable to estimates for untagged fish, further suggesting that the capture, handling, and tagging methods used were relatively benign. Identifying the primary components of the run (including both major and minor stocks) and determining site-specific utilization patterns can fundamentally enhance salmon management in large river basins, and facilitate research and conservation efforts.