This paper presents a watermarking technique for intellectual property protection (IPP) of circuits based on the residue number system (RNS). This technique relies on embedding a digital signature in non used cells of look-up tables of RNS-based designs at HDL design level; this enables the protection of author rights in the development and distribution of these designs as reusable modules (IP cores) in an efficient and transparent way. The embedded signature uniquely identifies both the design origin and the recipient, while being difficult to detect and/or remove, its extraction requires minimal modifications to the system. The presented IPP scheme has been implemented on a variety of FPL devices, not disrupting the functionality neither significantly degrading the performance of the example systems