This study provides new stratigraphic data and identifications for fossil marine mammals from the Monterey Formation in the Capistrano syncline, Orange County, California, showing that there are two distinct marine mammal assemblages. Until now, marine mammals from the Monterey Formation of Orange County have been considered to represent a single assemblage that is 13.0–10.0 Ma in age. By combining data from diatoms with the geographic positions of sites, faunal analysis, and data from the literature, we can assign 59 sites to three main levels: the lower part (ca. 16–13 Ma), the middle part (ca. 13–10 Ma), and the upper part (ca. 10–8 Ma). We assigned 308 marine mammal specimens to 38 taxa, resulting in 97 occurrences (unique record of a taxon for a given site). Of the 38 taxa we identified within the study area, 15 taxa are restricted to the lower part of the Monterey Formation, 15 are restricted to the upper part of the Monterey Formation, eight were found in both, and none has yet been reported from the middle (possibly condensed) section. Six of the eight taxa that occur in both the lower and upper parts of the Monterey Formation are higher-level taxa, which accounts for their broad temporal range. The recognition of two distinct marine mammal assemblages in the Monterey Formation of Orange County is an important step toward a better-calibrated sequence of faunal evolution in the region while improving the utility of marine mammals for regional biostratigraphy.