Iteroparity (repeat spawning) is a life history attribute with significant conservation value for at-risk populations of steelhead trout (Oncorhynchus mykiss). However, stock-specific rates of iteroparity and abundance of post-spawned steelhead “kelts” can be difficult to monitor in large river systems where multiple populations are commonly encountered as aggregated mixtures. We used genetic mixed-stock analysis (MSA) to determine steelhead origins and tested for stock-specific differences in the prevalence of an iterparous reproductive strategy. Steelhead from the Snake River, USA were sampled as “returns” migrating upstream to spawn and as emigrating post-spawned “kelts”. Fish were assigned between two regions that are characterized by predominant run-type. We observed a larger overall proportion of kelts from region-1 (putative-A run; 82%) compared to kelts from region-2 (putative B-run; 18%), but returns from region-2 (30%) were nearly twice as abundant as kelts. Female kelts were predominant throughout the basin, occurring in similar proportions between regions (72% region-1, 77% region-2). The inferred ocean age distribution of kelts was distinct between regions, and regional differences in body size and emigration timing were significant (P < 0.0001). Although the ocean age-classes for kelts and returns within the same region were similarly distributed, kelts were significantly smaller in average body size compared to returns, and the results were temporally consistent. The association between body size and post-spawn survival suggests that strategies to improve overall recovery of steelhead, such as artificial reconditioning, may achieve greater success by targeting smaller kelts. Moreover, monitoring of post-spawn survival, and repeat spawning potential will likely benefit from MSA to augment demographic information and improve the accuracy of differentiating among specific stocks or regions.