Major and trace chemical elements from eleven Lower Pleistocene bentonite deposits from Eastern Milos Island, Aegean, Greece, were used for geochemical fingerprinting of the bentonites, by means of scatter binary and ternary plots and canonical discriminant analysis. The trace elements were selected according to their immobility during bentonite formation and subsequent hydrothermal alteration. The bentonites can be separated into at least four geographically distinct groups, each consisting of materials with similar geochemical affinities. The deposits of each group were derived from protoliths erupted from different volcanic centres, suggesting the existence of at least two distinct volcanic provinces, having rhyolitic and andesitic affinities respectively. Several deposits consist of more than one bentonite horizon, indicating that in some volcanic centres the character of volcanism changed with time. Geochemical fingerprinting, supplemented with geological, mineralogical, and textural evidence, may be useful for correlation and exploration of bentonites, in terrains with complex geological histories.