Transdisciplinary research that crosses disciplinary boundaries and includes stakeholder collaboration is increasingly being used to address pressing and complex socio-ecological challenges in the Anthropocene. In fisheries, we see transdisciplinary approaches being employed to address a range of challenges, including bycatch where fine-scale data are collected by fishers to help advance spatial approaches in which fishing effort is shifted away from bycatch hotspots. However, the spatio-temporal overlap of morphologically undistinguishable fish stocks, some of which are depleted, is a major concern for some fisheries, including the Pacific Northwest troll Chinook salmon (Oncorhynchus tshawytscha) fishery. In this study, we develop and evaluate a transdisciplinary approach to avoid bycatch in the commercial Chinook salmon troll fishery off northern and central Oregon. Based on a unique genetic dataset collected by fishers, fine-scale patterns of stock distribution and spatial stock overlap were assessed. Two hotspots of weak Klamath stock in the study region were identified and related to bathymetry. Results were then fed into a simple bioeconomic model to evaluate costs and benefits of reallocating effort under two scenarios of allowable catch of a weak stock (Klamath). The scenarios demonstrate that effort reallocation could lead to a reduction in Klamath catch as well as to increases in net profit, but outcomes depend on the distance from the fleets' home port to the new fishing area. The output of the model at its current stage should be regarded strategically, providing a qualitative understanding of the types of best fleet strategies. Despite some challenges in transdisciplinarity discussed in this study and the present limitations to incorporate fine-scale changes of Chinook salmon stock distributions in management regulations, we contend that this approach to research has the potential to lead to improved management outcomes.