The genomics revolution has sparked interest in using our increased understanding of the loci involved in phenotypic variation and adaptation to advance the conservation of biodiversity. Despite much interest and discussion, it remains unclear whether, when, and how such analyses should be used to guide conservation action. Such 'gene-targeted' conservation strategies, while promising, are complicated by several factors including the complex genomic architecture of phenotypic variation and the strong potential for undesirable outcomes such as the loss of genome-wide genetic variation and evolutionary potential. We caution against relying on gene-targeted approaches as a conservation silver bullet and propose rigorous criteria to identify situations where gene-targeted approaches are likely to benefit conservation.