Affinity separation with magnetic beads is an important and widely used technique for DNA computing. We have designed and implemented an experimental lab-on-a-chip module for affinity-bead separation for DNA-based concept learning. Magnetic beads with DNA-probe sequences immobilized on their surface were used to select target strands, and these beads are restrained in the channel by a permanent magnet on top of the module. The separation process consists of two steps, i.e. hybridization and denaturation. We confirmed the separation process by a mixed solution that contains FITC modified strands, and measured the yield by UV spectrophotometer. The experimental results demonstrate a successful separation of the mixed DNA.