We introduce credal two-sample testing, a new hypothesis testing framework for comparing credal sets -- convex sets of probability measures where each element captures aleatoric uncertainty and the set itself represents epistemic uncertainty that arises from the modeller's partial ignorance. Classical two-sample tests, which rely on comparing precise distributions, fail to address epistemic uncertainty due to partial ignorance. To bridge this gap, we generalise two-sample tests to compare credal sets, enabling reasoning for equality, inclusion, intersection, and mutual exclusivity, each offering unique insights into the modeller's epistemic beliefs. We formalise these tests as two-sample tests with nuisance parameters and introduce the first permutation-based solution for this class of problems, significantly improving upon existing methods. Our approach properly incorporates the modeller's epistemic uncertainty into hypothesis testing, leading to more robust and credible conclusions, with kernel-based implementations for real-world applications.