Methods for integrating digital watermarks into holograms, watermarked hologram structures, and related applications. One method creates a watermark image, and then embeds the watermark image into a holographic structure. The holographic structure is created using computer generated holography to create a digital representation of the holographic structure. This digital representation is recorded on a physical substrate using optical techniques or microlithography. As an alterative, a watermark signal is embedded in a physical holographic structure by embedding the signal into an image that is optically merged with the holographic structure as it is optically recorded, or by embedding the signal into an image or physical model from which the holographic structure is formed. Another approach the creates a halftone watermarked image, and forms the halftone watermarked image in the hologram by creating hologram dots corresponding to the dots in the halftone watermarked image.