Vessel trajectory prediction (VTP) plays a critical role in maritime safety and intelligent navigation. Existing methods struggle to simultaneously capture long-term dependencies and nonlinear dynamic patterns in vessel movements. To address this challenge, we propose MKAIS, a novel trajectory prediction model that integrates the selective state space modeling capability of Mamba with the strong nonlinear representation power of Kolmogorov–Arnold Networks (KAN). Specifically, we design a feature-separated embedding strategy for AIS inputs (longitude, latitude, speed over ground, course over ground), followed by an MKAN module that jointly models global temporal dependencies and nonlinear dynamics. Experiments on the public ct_dma dataset demonstrate that MKAIS outperforms state-of-the-art baselines (LSTM, Transformer, TrAISformer, Mamba), achieving up to 16.65% improvement in the Haversine distance over 3 h prediction horizons. These results highlight the effectiveness and robustness of MKAIS for both short-term and long-term vessel trajectory prediction.