The rapid development of Large Language Models (LLMs) for code generation has transformed software development by automating coding tasks with unprecedented efficiency. However, the training of these models on open-source code repositories (e.g., from GitHub) raises critical ethical and legal concerns, particularly regarding data authorization and open-source license compliance. Developers are increasingly questioning whether model trainers have obtained proper authorization before using repositories for training, especially given the lack of transparency in data collection. To address these concerns, we propose a novel data marking framework RepoMark to audit the data usage of code LLMs. Our method enables auditors to verify whether their code has been used in training, while ensuring semantic preservation, imperceptibility, and theoretical false detection rate (FDR) guarantees. By generating multiple semantically equivalent code variants, RepoMark introduces data marks into the code files, and during detection, RepoMark leverages a novel ranking-based hypothesis test to detect model behavior difference on trained data. Compared to prior data auditing approaches, RepoMark significantly enhances data efficiency, allowing effective auditing even when the user's repository possesses only a small number of code files. Experiments demonstrate that RepoMark achieves a detection success rate over 90\% on small code repositories under a strict FDR guarantee of 5\%. This represents a significant advancement over existing data marking techniques, all of which only achieve accuracy below 55\% under identical settings. This further validates RepoMark as a robust, theoretically sound, and promising solution for enhancing transparency in code LLM training, which can safeguard the rights of code authors.