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Fishing impacts biodiversity on multiple levels, potentially resulting in unintended feedbacks to the economic performance of the fishery over time. For example, targeting observable traits within a population can impact genetic diversity and targeting valuable species can impact biodiversity at the ecosystem level. The bioeconomic literature, however, has given little attention to the effect of fishing on population diversity, even though population diversity contributes to ecosystem services and estimates of population extinction rates are three orders of magnitude higher than species extinction rates. Here we develop a stochastic bioeconomic model that links the harvest of multiple salmon populations in a single commercial fishery to the trajectory of population diversity in a salmon stock complex. We parameterize our model with biological and economic data from the Copper River Chinook salmon fishery. We show that markets can incentivize the degradation of population diversity, reducing infra-marginal fishery rents, and increasing variability in economic returns. We also show that second-best management can conserve population diversity and improve welfare. Furthermore, depending on fishermen's time preferences, this management strategy is potentially self-financing.