Paper-based digital microfluidic biochip (PB-DMFB) technology provides a promising solution to many biochemical applications. However, the PB-DMFB manufacturing process may suffer from potential security threats. For example, a Trojan insertion attack may affect the functionality of PB-DMFBs. To ensure the correct functionality of PB-DMFBs, we propose a watermarking scheme to hide information in the PB-DMFB layout, which allows users to check design integrity and authenticate the source of the PB-DMFB design. As a result, the proposed method serves as a countermeasure against Trojan insertion attacks in addition to proof of authorship.