Fish species diversity can be lost through interacting stressors including habitat loss, stocking and overfishing. Although a multitude of stressors have played a role in the global decline of coregonid (Coregonus spp.) diversity, a number of contemporary studies have identified habitat loss stemming from eutrophication as the primary cause. Unfortunately, reconstructing the role of fishing and stocking practices can be difficult, because these records are incomplete or appear only in hard-to-access historic grey literature. Based on an illustrative set of historic and contemporary studies, we describe how fisheries management practices may have contributed to coregonid diversity loss in European and North American lakes. We provide case studies examining how fishing and stocking may reduce coregonid diversity through demographic decline and introgressive hybridization. In some lakes, fisheries management practices may have led to a loss of coregonid diversity well before issues with habitat degradation manifested. Our review suggests that fish conservation policies could beneficially consider the relative importance of all stressors, including management practices, as potential drivers of diversity loss.