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Run-timing in salmonids is a prime example to study adaptive complexity in an iconic, culturally and economically important species. The Eel River in Northwestern California represents the southernmost extant population of summer-run steelhead in North America and is at the near-limit of the species’ thermal tolerance. It therefore presents an ideal location to examine the genetic basis for run-timing variations. Here we examine a number of issues related to steelhead conservation: 1) the extent to which upstream passage is blocked by ostensible physical barriers to dispersal; 2) spawning and rearing distribution of the two run-timings; 3) distribution of resident and anadromous genotypes; and 4) genetic diversity in a population of resident trout isolated above an impassable dam for nearly a century. Using Rapture (RAD Capture), we called genotypes at the region diagnostic for run-timing (GREB1L) and the region strongly associated with residency/anadromy in steelhead (OMY5). Remarkably, we concluded steelhead are passing a waterfall that has been managed as a complete barrier to anadromy. We also observed distinct spatial segregation between winter and summer-run steelhead in both the Middle Fork Eel and Van Duzen Rivers. Finally, we found evidence that prior to dam construction, summer-run steelhead inhabited the upper mainstem Eel, and that both life-history and overall genetic diversity are currently maintained in the resident trout population. Resident trout above the dam are well-suited to re-colonize the upper watershed if upstream passage were to be restored through the upcoming FERC re-licensing process.