Research into lab-on-a-chip multiplexed bioassays has focused on libraries of biochemical probes, indexed by optically encoded micron-sized labels. However, few current methods have reconciled large multiplexing capability with a rapid detection system amenable to miniaturization. Magnetic identification of labels provides a strong candidate solution to this problem, yet no proposed single-label magnetic detection system can both read and encode magnetic labels. We present a magnetic multiplexed assay in lab-on-a-chip format which identifies target biomolecules from the hybridization results by reading encoded magnetic beads. We show that a microfabricated magnetoresistive ring-shaped sensor can read the magnetic moments of individual commercially available paramagnetic beads using an active digital technique. This work provides proof of principle for a new approach to magnetic labeling of biomolecules for high-throughput bioassays.