The marine engine is a complex-structured multidisciplinary system that operates in a harsh environment involving high temperatures and pressures and gas/fluid/solid interactions. Many malfunctions and faults can occur to the marine engine and efficient condition monitoring is critical to ensure the expected performance. In this paper, a marine engine test rig is established and its process data are recorded, including various temperatures and pressures. Two data-driven models, i.e., principal component analysis and the sparse autoencoder, and a physics-based model are applied to the marine engine for two classic faults, i.e., lubrication oil filter blocking and cylinder leakage. Comparative studies and discussions are conducted regarding their performance in terms of anomaly detection and fault isolation. The data points collected for the filter blocking fault are generally two times higher than the fault thresholds set by the data-driven models. In the physics-based model, it is observed that the lubrication oil pressure falls from the predicted 3.2–3.8 bar to around 2.3 bar. For the cylinder leakage fault, the fault test data are nearly four times higher than the thresholds in the data-driven models. The exhaust gas temperature of the leaked cylinder falls from an estimated 150–200 °C to about 100 °C. The transferability and interpretability of these models are finally discussed. The findings of the present study offer insights into the two types of models and can provide guidance for the effective condition monitoring of marine engines.