Trajectory inference seeks to recover the temporal dynamics of a population from snapshots of its (uncoupled) temporal marginals, i.e. where observed particles are \emph{not} tracked over time. Lavenant et al. (2023) addressed this challenging problem under a stochastic differential equation (SDE) model with a gradient-driven drift in the observed space, introducing a minimum entropy estimator relative to the Wiener measure. Chizat et al. (2022) then provided a practical grid-free mean-field Langevin (MFL) algorithm using Schrodinger bridges. Motivated by the overwhelming success of observable state space models in the traditional paired trajectory inference problem (e.g. target tracking), we extend the above framework to a class of latent SDEs in the form of \emph{observable state space models}. In this setting, we use partial observations to infer trajectories in the latent space under a specified dynamics model (e.g. the constant velocity/acceleration models from target tracking). We introduce PO-MFL to solve this latent trajectory inference problem and provide theoretical guarantees by extending the results of Lavenant et al. (2023) to the partially observed setting. We leverage the MFL framework of Chizat et al. (2022), yielding an algorithm based on entropic OT between dynamics-adjusted adjacent time marginals. Experiments validate the robustness of our method and the exponential convergence of the MFL dynamics, and demonstrate significant outperformance over the latent-free method of Chizat et al. (2022) in key scenarios.