Protecting endangered wildlife from illegal poaching presents a critical challenge, particularly in vast and partially observable environments where real-time response is essential. This paper introduces a novel Expectation-Maximization (EM) based latent variable modeling approach in the context of Multi-Agent Reinforcement Learning (MARL) for Unmanned Aerial Vehicle (UAV) coordination in wildlife protection. By modeling hidden environmental factors and inter- agent dynamics through latent variables, our method enhances exploration and coordination under uncertainty. We implement and evaluate our EM-MARL framework using a custom simulation involving 10 UAVs tasked with patrolling protected habitats of the endangered Iranian leopard. Extensive experimental results demonstrate superior performance in detection accuracy, adaptability, and policy convergence when compared to standard algorithms such as Proximal Policy Optimization (PPO) and Deep Deterministic Policy Gradient (DDPG). Our findings underscore the potential of combining EM inference with MARL to improve decentralized decision- making in complex, high-stakes conservation scenarios. The full implementation, simulation environment, and training scripts are publicly available on GitHub.