Atocetus are usually assigned to the Kentriodontidae, but was later shown in a cladistic analysis to be a member of Pontoporiidae.
Although Atocetus and other pithanodelphinines are usually assigned to Kentriodontidae, the cladistic analysis of Lambert et al. However, a subsequent cladistic analysis by Post et al. (2017) recovers Atocetus as a member of Pontoporiidae, which includes the franciscana. 
