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How do we compare between hypotheses that are entirely consistent with observations? The marginal likelihood (aka Bayesian evidence), which represents the probability of generating our observations from a prior, provides a distinctive approach to this foundational question, automatically encoding Occam's razor. Although it has been observed that the marginal likelihood can overfit and is sensitive to prior assumptions, its limitations for hyperparameter learning and discrete model comparison have not been thoroughly investigated. We first revisit the appealing properties of the marginal likelihood for learning constraints and hypothesis testing. We then highlight the conceptual and practical issues in using the marginal likelihood as a proxy for generalization. Namely, we show how marginal likelihood can be negatively correlated with generalization, with implications for neural architecture search, and can lead to both underfitting and overfitting in hyperparameter learning. We also re-examine the connection between the marginal likelihood and PAC-Bayes bounds and use this connection to further elucidate the shortcomings of the marginal likelihood for model selection. We provide a partial remedy through a conditional marginal likelihood, which we show is more aligned with generalization, and practically valuable for large-scale hyperparameter learning, such as in deep kernel learning.