Fundamental selectivity limits of quantum control are pushed by introducing laser driven optimal dynamic discrimination to create distinguishing excitations on two nearly identical flavin molecules. Even with modest spectral resources, significant specificity is achieved with optimal pulse shapes, which amplify small molecular differences to create distinct, identifying signals. Rather than being a hindrance, system complexity appears to aid the control process and augments control field capability, which bodes well for implementation of quantum control in a variety of demanding applications.