Variations in the shape and size of teeth have been associated with changes in enamel ultrastructure across odontocetes. Characterizing these features in extinct taxa can elucidate their functional morphology and feeding strategy, while also shedding light into macroevolutionary patterns during the evolutionary history of cetaceans. This study aimed to (1) describe the enamel and dentine ultrastructure of the Early Miocene odontocetes Notocetus vanbenedeni and Phoberodon arctirostris from Patagonia (Argentina) and (2) quantify tooth and enamel ultrastructure morphological disparity among odontocetes. Enamel was predominantly prismatic, thin in the anterior tooth of N. vanbenedeni and P. arctirostris; whilst thick on the posterior tooth of N. vanbenedeni. Together with skull morphology, data suggests a raptorial feeding strategy for P. arctirostris and a combination suction feeding method for N. vanbenedeni. Statistical analyses supported these inferences, indicating that enamel characters are useful for paleoecological research. Morphological disparity analyses showed that extant odontocetes occupy a larger morphospace and have more disparate morphologies, whilst extinct odontocetes were more similar among each other than with the extant group. There was no clear phylogenetic-based grouping, suggesting that tooth and enamel ultrastructure disparity were mainly driven by ecological pressures. These results highlight enamel ultrastructure as a source for broader-scale paleoecological studies in cetaceans.