An automated batch identifier registration and embedding system for media signals, such as image, video and audio files. A batch identifier registration system enables a user to submit a request for a batch of unique identifiers to be embedded in media signals. The user submits a request for a batch of IDs. The batch registration system verifies the accuracy of the request, sends a confirmation, allocates IDs, creates corresponding entries in a registration database, and creates embedder files used in a batch embedding process. The user may then submit a request for embedder files. To perform automated batch embedding, a watermark embedder takes the embedder files and corresponding list of media signal files as input and automatically embeds identifiers supplied in the embedder files into corresponding media signal files.