-- Certifying safety in dynamical systems is crucial, but barrier certificates -- widely used to verify that system trajectories remain within a safe region -- typically require explicit system models. When dynamics are unknown, data-driven methods can be used instead, yet obtaining a valid certificate requires rigorous uncertainty quantification. For this purpose, existing methods usually rely on full-state measurements, limiting their applicability. This paper proposes a novel approach for synthesizing barrier certificates for unknown systems with latent states and polynomial dynamics. A Bayesian framework is employed, where a prior in state-space representation is updated using input-output data via a targeted marginal Metropolis-Hastings sampler . The resulting samples are used to construct a candidate barrier certificate through a sum-of-squares program. It is shown that if the candidate satisfies the required conditions on a test set of additional samples, it is also valid for the true, unknown system with high probability. The approach and its probabilistic guarantees are illustrated through a numerical simulation. Ensuring the safety of dynamical systems is a critical concern in applications such as human-robot interaction, autonomous driving, and medical devices, where failures can lead to severe consequences. In such scenarios, safety constraints typically mandate that the system state remains within a predefined allowable region. Barrier certificates [1] provide a systematic framework for verifying safety by establishing mathematical conditions that guarantee that system trajectories remain within these regions.